Hacker Chronicles 2/HACKER2.BIN/522.MANUAL

Text File | 1993-06-29 | 107KB | 2,123 lines

                                                DrawMap manual
                                                   ver 2.2



                                                 Teemu Teeri
                                                    1991


First things first:


The installation of DrawMap is described in the last part of this
manual, Appendix F.



Please note:

         This manual lacks all figures and tables.

         If you want to receive a printed manual and the latest
         update of DrawMap the shareware fee is $45.

         Please send check or money order to:

         Teemu Teeri
         Institute of Biotechnology
         P.O. Box 45
         FIN-00014 University of Helsinki
         Finland





Contents

Chapter 1
         Introduction
                 What is DrawMap and what are plasmid maps
                 How does DrawMap work

Chapter 2
         Using DrawMap - section by section
                 Section 0  -  Quit the program
                 Section 1  -  Draw a picture of the workfile
                          plasmid
                 Section 2  -  Show restriction data from the
                          workfile plasmid
                 Section 3  -  Get a new workfile
                 Section 4  -  Prepare a workfile from DNA
                          sequence
                 Section 5  -  Edit the workfile
                 Section 6  -  Save the workfile
                 Section 7  -  Change the default drive and file
                          directory

Chapter 3
         The EDIT section
                          FILENAME; PLASMID NAME; SIZE; FORM; ARC
                          DEFINITIONS; ARCS; GENES; SITES; SUPPRESSION
                          LIST; PICTURE COMPONENTS; COMMENTS
                 CLONING
                          INSERT; DELETE; REPLACE; ROTATE; MIRROR
                          IMAGE

Chapter 4
         The RESTRICTION DATA section

Chapter 5
         The DNA SEQUENCE section

Chapter 6
         The DRAW section

Chapter 7
         Customizing DrawMap


The SETUP section
                          COLORS; DEFAULT SETTINGS; PLOTTER DRIVERS
                 PLOTTER DRIVERS
                          Screen - circle only; Screen - full drawing;
                          Screen - high resolution; BBC SE284 plotter;
                          HPGL compatible plotter; Epson compatible
                          matrix printer; LaserJet II compatible
                          printer; PostScript printer; DeskJet printer

Appendix A
         Editing and creating DNA size standard files
         (.STD files)

Appendix B
         Editing and creating restriction enzyme files
         (.ENZ files)

Appendix C
         Modifying the DMDISP.TXT file

Appendix D
         The structure of the .MAP files

Appendix E
         The DrawMap character set

Appendix F
         Installation of DrawMap


Chapter 1

Introduction

What is DrawMap and what are plasmid maps

    Genetic engineering is a collection of techniques for a
molecular geneticist to make specific combinations of genetic
elements, analyze them and finally transfer them to the host
where he wants to study their effects. Genes and other genetic
elements consist of DNA, whose specific sequence of nucleotides
gives the stretch of this macromolecule its biological meaning.
DNA is also a substrate for various enzymes, with which it is
possible to cleave, modify and join the molecules in a
predetermined way and these biochemical reactions form the core
of genetic engineering.
    The geneticist does not usually synthesize himself the
molecules he combines, but takes use of the ability of the
bacterial cells to do the job. The DNA sequence of interest is
joined to other sequences that determine that the molecule will
be replicated in the bacterial cell. These self replicating,
usually circular DNA molecules are called plasmids. Many plasmids
exist in natural isolates of bacteria and hold genes for
resistance against specific antibiotics, for example. The
molecules that are designed to be able to carry foreign sequences
(inserts) are themselves combinations of sequences in natural
plasmids and other sources, and are often called gene vectors.
Besides plasmid vectors, the molecular geneticists also use
vectors derived from bacteriophages, especially the lambda phage.
Whereas plasmids are circular molecules, the lambda phage is
linear (the ends, however, do meet during the life cycle of the
phage).
   The sequence of nucleotide bases in a DNA molecule can be
determined by biochemical methods. Another important way to
document a DNA molecule is to show the physical map for
recognition sites for DNA cleaving enzymes. These enzymes, called
restriction enzymes due to their original biological role, can
detect a specific sequence of bases on a DNA molecule and cleave
the molecule, usually inside this recognition sequence. The
length  of the recognition sequence varies most often between 4
and 6 base pairs, determining also how often, on average, the
enzyme will cut "random" DNA sequence.
    A wide collection of restriction enzymes with different
recognition sites are known and commercially available. These
enzymes form the tools to cut out predetermined pieces of the DNA
molecule, which subsequently can be joined with another enzyme,
DNA ligase. Therefore a map of the restriction enzyme recognition
sites ("restriction sites") is very important to the user. The
restriction sites form the physical frame for a plasmid map. In
that frame, the geneticist can orient stretches of DNA he knows
to have biological function, such as genes and gene expression
control elements.
    The task of drawing a tidy plasmid map in scale is not
excessively complicated but does require some time and effort of
concentration. Therefore, the drawing of a proper and useful
plasmid map is often delayed and a good map is not available
during the period of work when it might be needed most.   DrawMap
is a program that produces tidy, in scale drawn plasmid maps for
the everyday use of the genetic engineer and, in the end, the
final maps for his publications. The program supports a variety
of plotting devices ranging from matrix printers to pen plotters
and laser printers. Maps can also be drawn on the computer video
screen for a quick check of how the current construction will
appear.


How does DrawMap work

    Activities of the DrawMap program can be divided in two
parts: 1) collecting, editing and maintaining the data describing
the plasmid maps and 2) composing and drawing the map on the
physical device chosen. As for drawing the maps by hand, the
locations of the characteristics of the map are defined by their
base pair coordinates. These characteristics are of three kind:

1)       Point-like features on the map, typically restriction
         sites, called sites in the program. These are defined by
         their coordinates and can be given names. They are shown on
         the drawn map as marking lines perpendicular to the main
         circle and with their names and coordinates written also
         perpendicular to the main circle (Figure 1). There may be
         a large number of these sites and they often crowd in
         particular regions of the map. For this reason, their
         drawing is handled specially and they are spread in the
         crowded areas (see front cover).

2)       Area-like features on the map, typically genes and also
         called genes in the program. These are defined by their end
         coordinates and can be given names as well. They are drawn
         as arcs inside the main circle and either or both ends of
         the arc can have an arrow head (Figure 2). The name is
         written inside the arc and follows its direction. Unlike
         for sites, the coordinates of the genes are not shown on
         the final map. The gene arc can also have zero length,
         which makes this a second point-like feature on the map,
         but presented in a different way from the sites.

3)       The second type of area-like features on the map, typically
         indicating areas different in function (like genes or
         promoters) or origin (in a recombinant molecule), are
         called arcs in the program.  The arcs form the main circle
         of the plasmid map. They are defined by more parameters
         than the genes:
   a) end coordinates
   b) arrowhead and its direction at the ends
   c) breadth of the arc
   d) number of pen strokes within the breadth, leading to
   appearances from open box, through a striped box, to a filled
   box (Figure 3).
   Arcs do not have names like the genes.
    In addition to the three map characteristics mentioned above,
which can vary in number, the map has also a name and a total
size (in base pairs). The final drawing has space for comments
as well.
    All this data is entered and can be edited in the editing
section of the program. They can be stored on a disk or diskette
as a file for later retrieval. Thus, the user can have a
collection of his plasmid maps on disk.
    In real life, plasmids come in families and some maps may
have much in common. Therefore, the entering of the same parts
for many maps is duplicated work and it is much simpler to edit
an existing map to a new one. To facilitate this, the DrawMap
program has capabilities of deleting parts of the plasmid map or,
reversely inserting empty space to be filled in by new features
or parts of other maps composed with the DrawMap program. These
facilities simulate the way how new plasmids are constructed from
preexisting ones in the laboratory with the methods of DNA
cloning. In addition, it is always possible to edit, remove, or
add sites, genes or arcs on the map one by one.
    The genes and arcs are always entered in the editing section.
For sites, it is also possible to determine them directly from
a DNA sequence. To be able to do that, the program needs to now
a collection of restriction enzymes with their recognition sites.
Such collections are provided with the program and they can be
easily updated or created with a standard text editor.
    Besides drawing plasmid maps, the DrawMap program can also
do restriction enzyme digestion simulations with the plasmids.
This is related to the very common way of viewing isolated
plasmid molecules by digesting them with some restriction enzymes
and by visualizing the resulting fragments after separation by
gel electrophoresis.
    The newly created or edited plasmid map can be drawn on
screen at different resolutions (and speeds - inversely related
to the resolution) to check the result while editing. Finally,
the drawing can be directed to the hard copy device connected to
the computer (a pen plotter or a matrix or laser printer). The
plotter commands can also be stored in a file on the disk, from
where they can be imported to many modern text editors to be
included in a document as a figure. DrawMap has also a special
batch feature that allows several maps to be drawn in succession
automatically.


Chapter 2

Using DrawMap - section by section


    The DrawMap program is divided into sections, which the user
enters from the main menu (Figure 4). He can call the sections
either by pressing the section number or a key corresponding to
the highlighted character on the section name. Some sections are
small and simple like the one that allows you to change the
current drive and directory and others are large  and complex
like the editing section. In the following, we shall go through
the different sections and show what the user can do in them and
how to achieve it. Later chapters will describe in detail the
more elaborate sections. The sections are covered here in the
order of appearance on the menu. That, however, is not the order
in which they are usually needed.
General comments on keys:
    Nearly each section contains context sensitive help behind
the function key F1. In some sections, a more general help window
is initiated and in others, individual advice is provided on how
to respond to a prompted question.
    Another key used repeatedly in a similar way is the ESC key.
This key quits the current action, finishes compilations when
needed, and returns the user back to the previous level.
Logically, exit of the program from the main menu should take
place with the ESC key. However, to prevent accidental exit, this
does not take place and the user must use the Q key instead.
    Many times the user is asked a yes/no question. The answer
is provided by hitting the Y or N key. Some questions take also
RETURN for answer and use then the default choice. When more
choices are offered, they are indicated with the question.
    CTRL-G and CTRL-V function as editing keys when text data is
edited in different tables and boxes. CTRL-G deletes a character
at the cursor position and CTRL-V inserts a space character
(blank) at the cursor position pushing existing text
simultaneously forward.


Section 0  -  Quit the program

Purpose:         Exit to DOS.

Operation:          Communication in the main menu window.

Restrictions:             None

Notes:              If the workfile has not been saved, the DrawMap
                    program will prompt whether it will be OK to exit.



Section 1  -  Draw a picture of the workfile plasmid

Purpose:         DrawMap composes the plasmid map from the data in the
                 workfile and sends the graphical representation to the
                 physical device determined by the user.

Operation:          The main menu is left behind and a drawing menu is
                    opened (Figure 5). The user picks up the physical
                    device from the list by indicating its number. By
                    pressing the B key, the batch function is activated.
                    Instead of drawing the workfile map, DrawMap will
                    draw all maps found in the current directory one
                    after the other.



Restrictions:             1)       The workfile must represent a plasmid unless
                                   you have activated batch drawing.
                 2)       The user's computer must be equipped with the
                          hardware with which the indicated driver program
                          is designed to function. Failure in this respect
                          may lead to unpredictable results. In doubt, be
                          sure that the workfile is saved first.

Notes:                This section is described in detail in chapter 6.



Section 2  -              Show restriction data from the workfile
plasmid

Purpose:         The plasmid map files contain all the data to predict
                 band patterns in gel electrophoresis of restriction
                 enzyme digested plasmids. This section gives these
                 predictions, either as fragment lists or as simulated
                 gel images.

Operation:            The main menu is left behind. The user is prompted
                      with questions concerning which enzymes to use in
                      the digestions.

Restrictions:             The workfile must represent a plasmid (i.e., you
                          cannot use a blank map).

Notes:                This section is described in detail in chapter 4.




Section 3  -  Get a new workfile

Purpose:         The plasmid map under construction or which is
                 otherwise worked with is called the workfile plasmid.
                 In this section the user can pick up a new map saved
                 on the disk or, alternatively, start to construct a
                 new map.

Operation:            Communication takes place in the main menu window.
                      DrawMap prompts for the name of the new workfile.
                      List of all .MAP files in the current directory is
                      shown when the help key F1 is hit. You can load a
                      map file also from another directory by providing
                      a path, e.g. A:\MAPS\PBR322.

Restrictions:             The entered reply must be a legal DOS file name.
                          If you specify a path, the file must also exist.

Notes:                Taking a new workfile automatically abandons the
                      previous workfile. If it had not been saved, the
                      DrawMap program will comment on the situation. You
                      can withdraw from picking a new workfile by
                      entering a blank line. If the entered filename
                      corresponds to an existing file, that one is
                      retrieved as the workfile. If the file does not
                      exist, the work file represents a blank plasmid
                      map. The plasmid map files created by DrawMap have
                      usually .MAP  as their extension. This default
                      extension does not have to be entered.
                     If the help key F1 is hit after typing in
                 characters, not all .MAP files in the directory are
                 shown but only those whose filename will match for
                 their beginning the entered characters.



Section 4  -  Prepare a workfile from DNA sequence

Purpose:         Restriction sites on a DNA sequence can be searched in
                 this section in order to be used as a basis of a new
                 plasmid map.

Operation:            The main menu is left behind. The user is prompted
                      with questions concerning where to find the data
                      for the DNA sequence and the restriction enzyme
                      recognition sites (the enzyme data can also be
                      entered from the keyboard).

Restrictions:             The DNA sequence must exist on disk as an ASCII
                          file, from which only the letters A, C, G, and T
                          (either upper or lower case) are extracted.

Notes:                This section is described in detail in chapter 5.



Section 5  -  Edit the workfile

Purpose:         This section collects all the necessary data to build
                 a map. Editing of existing data is also
                 straightforward and DNA cloning can be simulated.

Operation:            The main menu is left behind. The user moves around
                      with arrow keys in a table of data which he can
                      edit.

Notes:                This section is described in detail in chapter 3.



Section 6  -  Save the workfile

Purpose:         The workfile is saved in the current directory.

Operation:            Communication in the main menu window.

Restrictions:             The workfile must represent a plasmid (i.e., you
                          can not save a blank map).

Notes:                If a file with the same name as the workfile
                      already exists in the current directory, the user
                      is prompted of whether it should be written over.
                      Usually the pre-existing file represents a previous
                      version of the same plasmid map. The previous
                      version is not destroyed. You can find it under the
                      name LASTMAP.BAK in your map directory. Only after
                      the next saving operation the data will be lost.
                      LASTMAP.BAK always contains the data of the latest
                      overwritten .MAP file. This makes it possible to
                      regret your savings.



Section 7  -  Change the default drive and file directory

Purpose:         Changes the disk drive and directory from where saved
                 plasmids maps are retrieved and where they are filed
                 when saving.

Operation:            Communication in the main menu window. DrawMap
                      prompts for new (drive and) directory.

Restrictions:             Entered reply must correspond to an existing
                          (drive and) directory.

Notes:                If you start DrawMap by entering a directory name
                      as a program parameter (by typing at the DOS prompt
                      e.g. DRAWMAP A:\MAPS), the program will change into
                      that directory while starting. For different users,
                      it is practical to have personal DOS batch files
                      that will take DrawMap directly into the correct
                      personal directory (see appendix E).





Chapter 3

The EDIT section

    This is the section of the DrawMap program with which the
user can build a new map or edit one built earlier. It also
allows the user to insert parts of other maps into the plasmid
or replace parts with those of other maps, much in a similar way
as plasmid construction is made by DNA cloning techniques in the
laboratory.
    In the edit section, the data forming the plasmid map is
presented as a series of tables. The user moves the cursor into
the tables and enters or edits the data there. Special keys move
the cursor and edit the data. These keys are collected in table
I and appear also on the screen when the help key F1 is pressed.
Each time the cursor exits a data table (which may contain only
one row of data), the entered data is checked. If it cannot be
interpreted in a sensible way, the cursor moves back to the
erroneous item. Also, data in some tables are compiled when the
cursor exits the table, e.g. restriction enzyme sites are ordered
in ascending order by their position coordinate. Many data tables
allow a long list of data items to be entered. In those tables,
the empty rows are hidden and more space is opened only when
needed. The whole editing screen, which scrolls up and down when
you move in it, is shown in figure 6.

FILENAME

    This holds the DOS filename for the plasmid map. The map will
be saved on the disk as a file under this filename. Therefore,
the text entered must follow the DOS file name rules, i.e.
contain up to eight characters, a period, and up to three
characters in the extension part. Using upper or lower case
letters here make no difference. If the period is left out, the
DrawMap program will add .MAP in the name. You can type in other
extensions if you wish, but it is practical to use the suggested
extension. Since the program knows to expect it also elsewhere
and you will save some typing.
   If you want to build a new map based on an old one, be sure
to change the filename in this table. Otherwise, when saving the
map, it will replace the previous one on the disk.

PLASMID NAME

    This is the name of the plasmid that is written in the center
of the map. You can enter any characters, including spaces and
special graphic characters here and they will appear as such on
the plasmid name. Please note that the standard IBM character set
has been modified in DrawMap to include important characters such
as the lower case lambda (■). However, these modified characters
appear on screen as unmodified. They are treated in a special way
only by the drawing procedures. The full available character set
is described in appendix D.


SIZE

    Here you can enter the size of a new plasmid. When editing
an existing map, you can not change the size by entering a new
value here. Instead, the deletion and insertion functions in the
cloning menu must be used.

FORM

    The form of the plasmid is either circular or linear (see
Figure 7). Internally the map is presented as a circle
independent of the form which means e.g., that in both cases the
coordinates zero and size refer to the same point and not to the
opposite ends of the linear form. The form is changed by hitting
the  key L or C when the cursor is on the appropriate row.

ARC DEFINITIONS

    This table holds reference data on how different areas on the
plasmid main circle are drawn. Each arc definition has a number
that is referred to in the following table ARCS. Different types
of arcs are formed by varying the three parameters: thickness,
lines and pen. The thickness or breadth uses as a unit the radius
of the circular map. Lines tells you how many equally spaced arcs
are drawn within the thickness. By determining two arcs, an open
box type arc is drawn and by determining many, a filled black box
is drawn. Between these two extremes, you can get striped arcs
(see Figure 3). The parameter pen is very device dependent. On
xy-plotters using real pens, it refers to the pen number on the
pen rack that the user fills according to his choice. On matrix
printers or lasers it refers to the thickness of the line (but
only in high resolution), and on screen devices, it refers to the
color (if available). In addition, pen number 0 is treated
differently in different devices. On xy-plotters it logically
means no pen but on matrix printers or lasers (only high
resolution again) it means extra thin lines (e.g., for miniature
maps). Therefore, if you want to leave part of the map blank
(Figure 8), do not define an arc type with pen=0 but lines=0.
Thickness=0, on the other hand, leads to a simple, single stroke
line.
    The program defines four predefined arc types: single, heavy,
double and broad double, which however can be modified freely.
The default definitions serve as starting points for users own
definitions which may amount up to 20 different. To change the
predefined types permanently, see appendix C.
    Still one word about pens. Genes and sites are also drawn by
a pen but they do not have a pen number definition in their
tables. Instead, genes are drawn with the pen of arc definition
number 2 and sites (as well as all the rest) with the pen of arc
definition number 1. Normally you don't need to be concerned
about this. Only when you want to play with different pens, it
is important to know this.

ARCS

    Varying arcs on the main circle of the plasmid gives
character and a clarified appearance for the map. Arcs are
defined by their startpoint, endpoint and kind - the latter
referring to the arc definitions described above. In addition,
the borderline between two arcs can be an arrowhead, either to
the left (counterclockwise) or to the right (clockwise). These
are added by using the > and < keys and can be removed by
pressing CTRL-A. The arrowhead is always drawn on the arc that
has larger thickness, defined in the arc definition table.
Normally the tip of the arrowhead is at the coordinate of the arc
junction, but on short arcs (appearing as triangles) it pushes
towards the arrow direction.
    Arcs are added to the arcs table freely. It is important to
know how they are compiled when the cursor leaves the table.
DrawMap program first creates a basic map with arc type 1 all
over. On top of this, it adds first the arc defined on the first
row of the table, then from the second row and so on, discarding
older definitions from areas covered by new ones. This means that
the arc table can change a lot when the user knows how to take
advantage of this compilation. Clearing the arc table is done
simply by adding a full length definition on the last line and
exiting the table.
    The length of each arc must be at least one base pair. An arc
with the same startpoint and endpoint coordinate is interpreted
to mean a full round arc (which also cancels all previous
definitions due to the way of compilation). Note that with genes,
exactly the opposite interpretation is done.

GENES

    Genes are defined by entering their startpoint, endpoint and
name (which may be blank). Either end can have an arrowhead that
has fixed direction: outward from the gene. The arrowhead is
added to either end by pressing the  < or > key while the cursor
is on the end coordinate and removed by pressing CTRL-A. In the
final map drawing, the name of each gene is written along the
gene arrow and centered in respect to it. For the characters to
be in a readable orientation, the name is written clockwise in
the upper half of the map and counterclockwise in the lower. The
direction is determined by the midpoint of the gene and is shown
as a plus or minus sign in the column D (for direction). In
special cases you can force the direction by entering a + or -
in this column. The program does the midpoint calculation only
when the column is left blank (an exception to this is when you
have done cloning). You can redo the calculation by entering a
space in column D and moving to another row. A gene with
startpoint and endpoint equal is considered to have a zero
length.

SITES

    Sites are typically recognition sites for restriction
endonucleases. They are considered point-like (although the
recognition sites really span 4-6 base pairs) and are defined by
their coordinate and name. The last column contains information
for the RESTRICTION DATA section only: sites marked as enzymes
are cut in a digestion simulation (see that section). All sites
are enzymes by default and can be changed to markers by pressing
CTRL-T at the appropriate site row.
    A practical feature while entering sites is that if the name
is left blank, it is copied from the previous row. Therefore, you
can enter all sites with same names sequentially by typing only
their coordinates and rely on their reordering after exiting the
table. However, this feature makes using blank site names
difficult. You can enter them by first opening extra space in the
table with the RETURN key and typing in the enzyme separately of
others. Upon exiting of the table the blank enzymes will be
ordered properly. However they are unstable: if you pass through
the table, they will get names of their predecessors on the
table. To obtain "stable" blank site names, you should use the
non-printable character with code 255 (see appendix E).

SUPPRESSION LIST

    You can suppress the drawing of particular map components by
changing their status on the list by pressing CTRL-S. For
example, if the coordinates are not accurate, it may be better
not to show them at all. The map and the comments can also be
framed - an option that you can choose here.

PICTURE COMPONENTS

    The appearance of the map can be modified by modifying the
size parameters for the various parts of the map. E.g., crowded
areas for genes are not resolved in a similar fashion than for
sites so that the only means to clarify them is to reduce the
character size. Note that you can also change the shape of the
characters (Figure 9). All units here are again parts of the map
radius. The default values to give "standard" maps are shown on
the right column and pressing CTRL-D here retains that value
instead of clearing the row.
    The last parameter, magnification, is very useful. The
default magnification (1.0) allows space for full length site
names (20 characters) and the map remains often unnecessarily
small. For each map, the program calculates the maximum
magnification that still retains all features within the borders
of the picture. However, this is only a clue and higher
magnifications are allowed but will lead to clipping off of parts
of the map.

COMMENTS

    Finally, the map has ten rows of space for comments that of
course are completely free in format. As with other default
settings in these tables, the comment field can hold as a
default, e.g. your address. See appendix C to define the defaults
used for all new maps.

CLONING

    Filling in of the tables described above takes place when a
new plasmid map is constructed from scratch. In real laboratory
life, new plasmids are constructed from preexisting ones by
recombining fragments of them. The DrawMap program can simulate
this kind of DNA cloning. The cloning section is entered from the
editing section by pressing the F2 key. The actual cloning
functions are INSERT, DELETE and REPLACE. The functions ROTATE
and MIRROR IMAGE found in this section as well, do not change the
content of the map.
    A cloning function is chosen by pressing the appropriate
number key. Before the cloning step is finished (i.e., during the
entry of the relevant coordinates), pressing ESC will lead to
cancellation of what was started. The operation of the cloning
functions is the following:

INSERT

    With this function it is possible to insert a foreign segment
at a particular coordinate on the map. If that coordinate
contains a site, the site will appear at both ends of the insert.
After the entry of the insertion coordinate, the user will be
asked for the source of the insert. Entering a blank line here
inserts a blank, featureless region on the map the length of
which is asked next. Alternatively, entering the name for an
existing plasmid map, the insert will be taken from that plasmid.
(If the source map file is not in the current directory, drive
and directory data can precede the file name. The extension .MAP
can be left out, e.g. C:\MAPS\PBR322). Again, coordinates to
define the insert are asked. It is important to enter first the
left coordinate (5' for the geneticist) and then the right (3')
coordinate. When the origin (coordinate zero) is included in the
map, the startpoint coordinate will be larger than the endpoint
coordinate. If the startpoint and endpoint coordinates are equal,
the whole source plasmid is inserted into the workfile plasmid.
    The orientation of the insert is defined next. Pressing + (or
RETURN) inserts the fragment in the same orientation as it is in
the source map and pressing - inserts it in the reverse
orientation.
    The INSERT function joins the ends of the insert to the
insertion coordinate on the current (workfile) plasmid. If the
joining point contains the same site (by name) on both maps, they
are fused to one, exactly like in DNA ligation. If the two sites
are different, they still are joined, but a new name for the
combined site is asked for. If you enter a blank line for the
name, the combined site is discarded.

DELETE

    The function DELETE is the reverse of the function INSERT.
You need to provide the startpoint and endpoint coordinates and
everything between these is removed from the map. The ends are
joined and if they contain the same site, that is retained at the
joining point. Again, if both ends do contain a site but they are
different, a new name for the combined site is asked.

REPLACE

    REPLACE is a combination of DELETE and INSERT. The segment
of the current plasmid to be removed is defined by its startpoint
and endpoint coordinates, as when using DELETE. The source of the
insert is entered exactly the same way as when using the INSERT
function. Also, sites at the joints are treated as in INSERT and
DELETE.

ROTATE

    ROTATE is a function with which you can rotate the map into
a new orientation. The program will ask which coordinate will
become the new origin (coordinate 0). After rotating, all
coordinates have new values.

MIRROR IMAGE

     MIRROR IMAGE function inverts the map. The axis of mirroring
is defined by entering a map coordinate.


    After each cloning function, the  user still remains at the
cloning window and can use any of the functions again. You return
to the EDIT section by pressing ESC. Similarly, the DrawMap MENU
is reached from the EDIT section by pressing ESC. The current
table is exited automatically before the EDIT section is left
behind.


Chapter 4

The RESTRICTION DATA section

    The point-like features called sites on the plasmid map are
typically recognition sites for restriction endonucleases,
specific enzymes that cut the DNA molecule at their recognition
site. The fragments produced can be separated according to their
size by using gel electrophoresis and visualized by staining with
particular dyes. This kind of fragment "fingerprint" is a routine
way to identify a preparation of plasmid molecules.
    The RESTRICTION DATA section calculates an ordered list of
the fragments produced by digestion with one or several
restriction enzymes. It can also simulate gel electrophoresis and
show on screen a simulated image of the electrophoretic analysis.
This allows easy comparison of the expected and actual
electrophoretic results.
    The section works by presenting questions to which the user
answers. The first question is whether the fragment list will be
sent to the parallel printer attached to the computer (in LPT1).
Allowable answers are Y for yes, N for no and F for printing the
list of the fragments but omitting the startpoint and endpoint
data for each of them.
    Next you enter the names of the enzymes in the simulated
digestion (corresponding to the sites on the map), each on a
separate row, i.e. separated by pressing the RETURN key. When all
enzymes are entered, press RETURN once more and the ordered list
of the fragments produced is shown. It is important to know how
the entered enzymes and the sites on the map are matched. The
program considers that the enzyme cuts the site if the site
contains the entered enzyme name as a part of it. In addition to
the normal one-to-one match, this means for example that the
enzyme 'Ava1' will cut also the site 'Sma1 Ava1'. However, you
must be careful since 'Hind' cuts both 'Hind3' and 'Hind2', which
perhaps was not the purpose. The entered enzyme name can have
trailing spaces. Therefore, if you enter 'Cla1   ', this cuts the
site 'Cla1' but not 'Cla1 (dam)'. From the above it is clear that
the spelling of the entered enzyme name must exactly match the
spelling of the sites and, also, that using upper or lower case
letters now does make a difference. To make all this easier, the
F2 key will list the different sites on the map with their exact
spelling. Beside the site name the number of its occurrence on
the map is shown and, also, the sites that were recognized in the
last digestion are highlighted.
    After calculating the fragment list, the program waits for
new enzymes for the next digestion. Before going forward you can
inspect the gel simulation by pressing the F3 key. The gel
simulation plots the fragments on the screen according to the
logarithms of their sizes (Figure 10). This is a reasonably good
simulation for a real gel. The smallest fragment visible at the
lower edge of the monitor is about 800 bp in size and the still
smaller ones run downwards out of the monitor. By pressing the
UP ARROW key you can compress the gel and see the smallest
fragments and correspondingly by pressing the DOWN ARROW key you
can stretch the gel and separate better the large fragments from
each other. This effectively simulates varying the concentration
of the gel matrix or run length of the electrophoresis.
    Beside the digestion pattern of your plasmid DNA, a DNA size
standard is shown. You can change the size standard by pressing
the F2 key. The size standards are held on disk as data files.
If you want to pick one of those, answer F to the first question.
A list of available standard files will appear on the screen and
you pick one by entering its name. (The extension .STD can be
left out.) On entering the RESTRICTION DATA section, DrawMap
automatically picks a predefined standard file. You can change
this in the SETUP section.
    Alternatively, you can enter the sizes of the fragments in
the standard from the keyboard. To choose this, answer K to the
first question. You can first give the standard a name that will
appear on the gel simulation (max 20 characters). Next the
fragments in the standard are entered in base pairs (in any
order) and finally, after entering a blank line to indicate that
all fragments are entered, you can give the list a file name (in
DOS format) if you want to save it on disk for later use.


Chapter 5

The DNA SEQUENCE section


    The EDIT section allowed the user to enter restriction enzyme
cut sites by their coordinates and names. This section allows a
very different but useful way to enter the sites, directly from
a previously recorded DNA sequence. (This section may be helpful
also in the primary analysis of DNA sequences.) The sequence must
be on the computer disk or diskette as a file consisting of ASCII
characters. Only the characters A, C, G and T (as well as N, and
X for unknown bases), either in upper or lower case, are recorded
and others are discarded. The other file needed is the file for
restriction enzymes and their cut sites. The DrawMap program
package contains two such files, the files ALL.ENZ containing
commercially available restriction enzymes and their recognition
sites and 6BASE.ENZ containing restriction enzymes with at least
six base pairs long recognition sequences. These files are text
files and they can be modified and edited with any standard word
processing program. (For details, see appendix B.)
    Unlike the DNA sequence, the list of restriction enzymes can
also be entered by hand from the keyboard. This is practical when
only a few enzymes need to be scanned. The entered list can also
be saved on disk for later use. A site for an enzyme in the DNA
sequence is scored when the recognition site of the enzyme
matches, base pair by base pair, a stretch in the DNA sequence.
The match is tried simultaneously also on the other strand of the
DNA molecule (not recorded but implicit by the biochemical
structure of DNA), unless this feature is disabled (see later).
    The site coordinate will be at the first base pair matching
the enzyme's recognition sequence. Note that this is not
connected to the actual cut site that varies depending on the
enzyme and is not known for all of them. If there was no workfile
map when this section was entered, one equal in size to the
length of the recorded DNA sequence will be created. However, if
a workfile exists, the new enzymes found in this section will be
put among the previously existing ones. The workfile plasmid
should not be smaller than the length of the recorded sequence!
If you intend to "clone" (insert) the recorded DNA sequence into
a preexisting plasmid, you should perform the following functions
first in the EDIT section cloning menu:
1.       Choose the site of insertion and rotate it to the desired
         location, usually to point zero. The first base pair of the
         recorded DNA sequence will have coordinate 1.
2.       If necessary, mirror image the map to get it in the desired
         orientation with respect to the DNA sequence. The recorded
         sequence cannot be mirrored, but you can mirror again the
         end result.
3.       Insert, at the chosen site of insertion, blank space
         corresponding in size to the length of the DNA sequence.
         Perhaps you also want to define its arc type and insert a
         gene arrow in it. See EDIT section for details.
    Now you have arranged blank space in your map, starting from
coordinate 1, and the site coordinates read from the DNA sequence
will fall in their right places.
    The DNA SEQUENCE section has two parts. The first part is
question-answer oriented and its purpose is to locate and read
the sequence and enzyme files. The second part is a list of all
enzymes from the enzyme file together with indication of how many
sites was found. These are usually far too many to be all
included in the map and part of the enzymes must be discarded.
This is done by moving around in the table with the arrow keys
and doing the decisions with special keys. Behind the help key
F1 is information about the special keys that can be used (see
also Table II) as well as on the color coding used in the enzyme
table.
    The first part starts by prompting for the name of the DNA
sequence file. If you use a DNA analysis software that produces
DNA sequence files with a standard file name, you can make
DrawMap to suggest this file name automatically (see the SETUP
section). The file name must be in DOS format and it may contain
drive and directory specifications. You will be returned to this
question until you enter a name for an existing file or press ESC
to return back to the main menu. When the program locates the
sequence file it reads it into the memory. The maximum length of
the sequence depends on how much free memory you have at the time
and can be increased by removing any memory resident programs.
    Only the characters corresponding to bases in the biochemical
structure of DNA are recorded, as well as two characters that can
be used to indicate unknown bases (that is A, C, G, T, N and X -
 either upper or lower case). There is one functional exception
to this: DrawMap stops to consider the line that contains the
first encountered non-base character (not counting numbers or
blanks). That string might be a name for the sequence. You will
be asked whether to skip it when reading the bases (then it is
a name and will be recorded as plasmid name if there doesn't
exist one already) or not (in which case the A's, C's, G's, T's,
N's and X's are extracted from it!).
    When reading is done, a short statistics is shown. In
addition to the number of base pairs recorded, the number of
blanks and digits encountered are show. Also, and very
importantly, the number of other characters is shown and if this
is not zero, the first forty are displayed. This list should be
empty and if it is not, it probably means that your DNA sequence
file was not what you thought it was. It may have contained also
amino acid sequence data or it may have been a completely
unrelated file. Note that in the string of other characters there
are no A's, C's, G's, T's, N's or X's - they have bee extracted
into the recorded sequence. When other characters are
encountered, the program asks whether you would start over.
Usually you should.
    Next step is the reading in of the enzyme file. If you have
the appropriate enzyme file on disk, press F in response to the
next question and enter the enzyme name. The list of the enzyme
files found in the \DRAWMAP directory is shown at the upper right
corner and again you can customize the program to offer you a
choice (see SETUP section). To access other enzyme files than
those listed, you must include (drive and) directory data (all
in DOS format, of course). Alternatively, you can enter the
enzyme list from the keyboard. You will be first asked for a name
for the enzyme and then its recognition site (upper and lower
case don't make difference). Many enzymes have several
possibilities for a match at a particular position. These are
coded by other alphabetical characters than A, C, G and T (See
table III) and you will get the list on screen by pressing the
help key F1. Note that all non-listed characters behave as the
character N and will match anything (type carefully!). The list
is ended by entering a blank line for the recognition sequence.
After that, you have a chance to save the list on disk with a
file name of your choice (but in DOS format). If the period in
the file name is left out, the default extension .ENZ will be
added. This is a practical way to enter short enzyme lists, but
for longer ones, see appendix B.
    Before the actual scanning you will be asked whether both
strands on the DNA sequence are scanned. This is a natural thing
to do for restriction enzymes (but, however, makes a difference
only in those few enzymes that do not have palindromic
recognition sites). The real meaning of the question is to allow
efficient "misuse" of the section. The "enzymes" do not
necessarily have to be restriction enzymes and the "recognition
sequences" what they were originally meant to be. You can scan
any kind of sequence matches (including mismatches, see table
III) on the recorded DNA sequence. If you scan for example for
ribosome binding sites or polyadenylation sites, only one strand
(the recorded strand) is meaningful to scan and in such a case
you answer NO to the last question.
    What happens next is that the screen changes and you start
to get an expanding list of the enzymes entered in the previous
part. Each enzyme will have a number attached to its left - that
indicates the number of sites found on the DNA sequence. There
is also color coding: the enzymes with no sites appear blue and
others green. (The color coding can be altered in the SETUP
section to fit your taste and screen.) When the list is through,
the bottom of the screen shows you the total number of found
sites, which often exceeds the upper limit of 150 allowed sites.
    The last enzyme will be highlighted and the cursor is at the
name. If you hit the arrow keys, the cursor will move to another
site. If you hit the - key, it will turn to red (or magenta) and
will become "unchosen". If you hit the + key, it will appear
green (or blue) again. The SPACE BAR key will toggle between
these two. This is how you choose and unchoose your enzymes. When
you unchoose an enzyme with found sites, you can see the total
number of sites change. If you unchoose an enzyme with no sites,
the total number of sites does not change of course, but the
operation still has meaning. The program lists in the comment
field of the map those enzymes that do not cut, but only those
that are chosen. (If the comment field already has text, the
enzymes will be put in areas of blank space. Note also that there
is no warning if all intended enzyme names do not fit in the free
space of the comment field.) Besides moving around with the
cursor keys and choosing or unchoosing individual sites, you can
also categorically unchoose all sites with more than a particular
number of sites by pressing a numerical key (See table II for all
the alternatives).
    Finally, when you are ready, press ESC to return to the main
menu. Be patient, the final processing of the wanted and unwanted
sites takes a short while.


Chapter 6

The DRAW section

    Entering this section brings you to a list of physical
plotting devices which is much of your own product when you chose
the devices in the SETUP section. You pick the one you want by
pressing the appropriate number key and what happens next depends
again on what you set up yourself. The descriptions of the
different devices supported and how they are installed are found
in the SETUP section.
    Below the list of the files there is the code B for batch.
By hitting this key, an indicator will switch on at the upper
left corner but nothing else happens. (You can toggle the
indicator on and off with the B key.) What batch does is that
instead of drawing the workfile plasmid map, the DrawMap program
will draw all the maps sequentially in the current directory. The
current directory is shown at the bottom of the screen and can
be changed in the main menu. This is very practical when you need
to produce a series of maps since normally you would have to
change the workfile between the maps. After batch drawing is
started, no user intervention is needed and tens of maps can be
produced automatically. Batch drawing can be used with any
physical device that itself does not need user action (like
changing of paper) between the drawing of successive pages. Also,
for the fun, drawing on screen can be run in batch. Each map is
shown for five seconds before the next is taken under processing.
    Error handling is different from normal when maps are drawn
in batch. Normally error messages are displayed on screen. When
BATCH is active, a special file named DMBATCH.LOG is created in
the directory where the map files to be processed are. That
contains a list of all the map files found, together with any
communication directed to the user. It is a good practice to
check this file after each run with BATCH on. The error messages
may be informative if you think that some maps are missing. Note
that when you draw maps in batch, only those files with the
extension .MAP will be recognized.
    Please  refer to the  SETUP section  to see the description
of each of the devices supported.


Chapter 7

Customizing DrawMap

     In the EDIT section it was described how the picture
component dimensions such as character size, length of the site
mark, magnification can be modified to obtain more appealing maps
or special effects. It is possible to incorporate modified values
in the DrawMap system as defaults that are used for each new map.
This is done by modifying the file which is used to form the
editing screen. This file (DMDISP.TXT) is a text file that can
be edited with a standard word processor. Besides modifying the
picture component dimensions, you can incorporate data beforehand
in the tables, in order to permanently define new arc type
definitions or alter the existing ones, include your name and
address to the comment box, or to determine which map components
are drawn (the suppression list). These modifications will affect
every new map composed, the old ones will not be touched.
    Also some other files used by the DrawMap program are plain
text files in order to make their customization easy. The list
of restriction enzymes with their recognition sites (the .ENZ
files) and DNA size standards for the gel simulation (the .STD
files) are such. In fact, the .MAP files themselves are text
files, too. It is not necessary to edit the .MAP files directly
but it indeed is possible and their readable structure makes it
easy for a foreign program to use them.
    The structures and instructions for the editing of these text
files are described in appendixes A-D.


The SETUP section

    In addition to the possibility of editing the text files, the
DrawMap program has within it a section to customize the screen
colors, some default file and directory names and, very
importantly, the list of plotter devices to draw the plasmid
maps. The SETUP section is not entered in a similar way as the
other sections. When starting the program, type DRAWMAP SETUP The
SETUP MENU is shown in Figure 11. You move the arrow to point the
item you want to customize and hit RETURN.
COLORS

    In the color customization a cartoon version of each DrawMap
screen appears, drawn in the present colors. You move the cursor
with the arrow keys and when you want to change the color of a
particular piece of text under the cursor, press the F1 key. On
top of the screen, a box with all the possible color combinations
will appear, the cursor blinking at the one corresponding to what
are the present colors and what you wanted to change. Again, use
the arrow keys to move the cursor on the color combination you
want and hit RETURN to change the color on the DrawMap screen.
If you are not satisfied, repeat the sequence. Sometimes, when
the colors are badly off the capabilities of your monitor (e.g.,
when you use a monochrome monitor), you may not see all the text
to be seen since some text is of the same intensity as the
background. By pressing the F2 key, you can remove all colors and
be sure to see everything that will need customization. Note that
some colors on the screen, especially backgrounds, go in groups
so that by changing the background of a particular item, also
backgrounds of other parts will be changed.
DEFAULT SETTINGS

    You can tell DrawMap in advance into which directory it
should switch into when starting. (This corresponds to changing
of the drive and directory from the main menu. If you give the
drive and directory as a program parameter, it overrides the
default setting described here.) Similarly, you can make the
program to pick or suggest a standard file for the reading of DNA
sequence, restriction enzymes or DNA size standard. This is done
by typing in the appropriate directories or file names on the
default settings screen (Figure 12).


PLOTTER DRIVERS

    When you install the DrawMap in your computer or when you get
new plotting equipment, you must define the plotter drivers. You
can have up to nine plotter drivers assigned from which to choose
(physically different devices or same devices with different
parameters). If you need something in excess to this, modify the
plotter drivers temporarily, for that run only, by exiting the
SETUP MENU with the ESC key instead of the F2 key after making
the changes. (F2 saves the setting on disk but ESC doesn't.)
    When you start to modify your plotter drivers, the first
screen shows the preexisting list of choices. Initially it will
contain only two different graphics screen drivers (Figure 13).
You can remove assigned drivers from the list with the F1 key.
To assign a new one, move the cursor to a free row and press
RETURN. The screen will change into a list of the different
plotter drivers programmed in the DrawMap Program (Figure 14).
They will be described in detail later in this chapter. Again,
by moving the cursor with the arrow keys and pressing RETURN, you
choose the device you intend to assign and the screen changes.
    On the last screen (Figure 15), you define the communication
parameters etc. Note that not all plotters will have the full
list of parameters depicted in Figure 15. E.g. for the screen
drivers the communication port ("device") need not to be
specified, nor the baud rate when you have chosen a parallel
port. The parameters not needed will simply not appear on the
screen.
    The first row is a description of the plotter device and it
initially shows what was on the device list (Figure 14). This
description will appear on the DRAWING MENU (Figure 5) and if you
choose several versions of the same plotter (e.g. with different
resolutions or communication ports), it is very important that
you edit the description to show the differences on the DRAWING
MENU. Also, instead of retaining something like "HPGL compatible
plotter", it might be more helpful for all users to type in the
name of the actual plotter you have.
    The device box determines at which communications port the
plotter is plugged in. The program supports two serial ports
(COM1 and COM2) and three parallel ports (LPT1, LPT2 and LPT3).
If you choose the serial port, you must also define the baud
rate, the parity, and the number of data and stop bits. The
format of this definition is the same as in the DOS command MODE
COM (please consult your DOS manual for details).
    The destiny of the data need not to be either of the
communications ports. It can also be a file on disk (or the NUL
device, i.e. nowhere - this has mostly meaning for testing the
program). If the entered text in the device box doesn't match to
any of the ports or the NUL device, it is taken as a file name.
The file name is checked for proper DOS format only when it is
used, so that you can leave the box also blank in order to direct
the data to a file the name of which is asked later when it is
needed. The directing of plotting data into a file is meaningful
when you use the HPGL or PostScript drivers. Many word processing
programs can pick up pictures composed by using these standard
plotter languages and therefore you can incorporate maps drawn
with the DrawMap program into your documents. This possibility
has been used extensively in the manual you are now reading. You
can direct data for the matrix and laser printers into a file as
well, but they will be more difficult to use and, do remember,
very large (up to one MB). The directioning of data into a file
can also be used as a universal device. If you enter, run time,
as a file name any of the port names or the null device mentioned
above (i.e. COM1, LPT1 etc.), the destiny will be the port or
null device designed. Note that the baud rate of the COM ports
will then be whatever it was set to be earlier.
    The model box is something which is very specific to each
plotter and appears only when there are different choices. For
HPGL plotters it refers to the orientation of the paper (portrait
or landscape) and you should choose the one that matches your
plotter. For the raster devices (matrix and laser printers) it
means resolution. Maps with coarser resolution are naturally
faster to produce and you may want to include them to make fast
draft maps. You choose the "model" by hitting a number key and
the box will automatically show the choice in readable language.
    Last on the list, you can order DrawMap to pause and wait for
a key stroke before it starts sending the data. Whether you need
this, depends on your particular arrangement of things.
Especially with xy-plotters (pen plotters) it may be wise to stop
to check that everything is ready before starting the drawing.
    When you exit this last screen, you will find the new plotter
incorporated on your plotter list. You can go on and assign new
plotters (or edit the parameters of the ones already assigned)
or retreat from the SETUP section by pressing repeatedly the ESC
key. Note that the changes made in the SETUP section are saved
only when you exit the SETUP MENU with the F2 key. If you exit
with ESC, they will affect only the current run of DrawMap.


PLOTTER DRIVERS

    The current version 2.1 of DrawMap contains nine different
plotter drivers. Three correspond to a graphics screen at
different resolutions (and speeds of use). All the screen drivers
can be used with the CGA, EGA, VGA and Hercules screens. The
drivers will be described in detail here.

Screen - circle only
    This is the coarsest resolution screen driver but fastest to
use. It draws only the arcs, genes and the site marks but leaves
away all text (Figure 16). If the monitor can use colors at the
320 x 200 resolution, use of different pens is shown as different
colors. Pen number 0 is not visible. The main use is to check
quickly the overall composition of the map.

Screen - full drawing
     This screen driver draws the whole map on screen with
comments and texts as they would appear in the final form (Figure
17). The highest available resolution of the monitor is chosen
and if this allows colors they are used as with the previous
driver. The high resolution screens (like the EGA and VGA) allow
resolving of the individual characters but with the CGA monitor
only a coarse general image can be obtained. In all cases this
driver is very useful in checking the actual positions of gene
names etc. on the map.

 Screen - high resolution
    The resolution of this screen driver is 640 x 874 pixels
independent of the monitor used. Instead, monitors with lower
resolution show only a window into the map which can be moved
with the arrow keys (Figure 18). The resolution giving
approximately even aspect ratio is chosen (i.e. showing a circle
mostly as round) and no colors are used. All pens draw similarly,
including pen 0. Although this screen driver is rather slow in
the standard PC computer, its resolution is sufficient to
visualize all details of the map on all monitors.
BBC SE284 plotter
    This is a specific driver for the BBC SE284 plotter. The
plotter can use several pens that are assembled on its pen rack
and referred to by their numbers. Pen number 0 means no pen at
all.

HPGL compatible plotter
    The Hewlett Packard Graphics Language (HPGL) is one of the
standard vector graphics languages used by many xy-plotters (pen
plotters). If your plotter can understand HPGL, choose this
driver. Because of its standard nature, the HPGL is suitable also
for other purposes. Many word processing programs can read HPGL
files and that makes it possible to include DrawMap maps in your
text documents directly, without scissors and glue. For that
purpose, direct the HPGL data into a disk file (see SETUP
section, PLOTTER DRIVERS). Xy-plotters use physical pens and the
pen numbers refer to different pens on the pen rack. Pen number
0 means no pen at all.

Epson compatible matrix printer
    Like HPGL, the Epson bit image mode code to make raster
images is kind of a standard since many different matrix printers
can emulate the Epson printer. The maximum resolution is rather
high (240 x 216 dots per square inch - the common laser printers
are 300 x 300) and the quality of the drawing is comparable to
one produced by a laser printer (see Figures 19 and 20). However,
the quality depends a lot on the particular printer used (its pin
head and paper feeding mechanisms). Since the matrix printer
lacks physical pens, the pen number refers here to the thickness
of the line. Pen number one is single dot thickness, two is two
dots and so on. With the Epson drive, the pen number 0 does not
show.

LaserJet II compatible printer
    As widely as the Epson bit image code is standard within
matrix printers, the code of the HP LaserJet II is a standard
among laser printers (and some others as well, such as the HP
DeskJet). The drawing is a raster image with resolution of 300
x 300 dots per square inch. Also in this drive the pen number
refers to line thickness but now so that pen number one means two
dots wide line, two is three dots wide and so on. The single dot
thickness is too thin for most cases, but you can produce it with
pen number 0 (e.g. for miniature maps). Therefore, in order to
use no pen at all for parts of the map, you must define Lines=0
in the arc type definitions (see EDIT section).

PostScript printer
    PostScript is a powerful "page description language". Many
laser printers use it but it is designed to be used with other
equipment as well. Several word processing programs can read
PostScript code and include figures made with the PostScript
language. PostScript is a very rich language and its vocabulary
include vector graphics commands which are the ones DrawMap uses
(Figure 20). Since PostScript is a vector language, a laser
printer equipped to understand it will produce maps far more
quickly than when a raster driver (LaserJet II) is used. The pen
numbers refer to line thicknesses exactly as in the LaserJet II
Driver. However, since the PostScript unit is not a dot, the line
width is defined as a real measure. This means in practice that
it is not dependent on the 300 x 300 resolution. The code
produced by DrawMap is Encapsulated PostScript, or EPS code.

DeskJet printer
    This driver produces optimized code for the HP DeskJet
printer. It is two to three times faster than the LaserJet II
driver.



Appendix A

Editing and creating DNA size standard files (.STD files)


    The RESTRICTION DATA section calculates the fragments
produced from the workfile plasmid when it would be digested with
the restriction enzymes indicated. The section can also show a
simulated electrophoresis gel where the fragments are shown
beside a known series of molecular weight (fragment length)
standards. The set of standard fragments varies between different
laboratories, but one user has usually a limited set of them. The
standard sets are saved on disk as text files and since they are
small, they are most easily created from within the DrawMap
program (see the RESTRICTION DATA section).
    The structure of the standard files (the .STD files) is,
however, simple and described here if the user wants to edit them
with a text editor. The first line contains the name of the
standard that appears as a title in the simulated gel. Its
maximum length is 20 characters. What follows, starting from the
second line, are the fragment lengths in base pairs. They should
be in descending order, at least so that the largest is the first
one. Be sure not to include extra lines or non-numerical data
(except in the first line). They will be ignored but not without
complaints. As an example, the set of fragments produced from the
phage lambda DNA, digested with the enzymes EcoR1 and Hind3, is
shown below. It is included in the DrawMap packet, named L-
EH.STD.


Lambda EcoR1+Hind3
21227
5143
4975
4271
3522
2023
1906
1584
1374
947
831
564
125



Appendix B

Editing and creating restriction enzyme files (.ENZ files)

    The DNA SEQUENCE section searches restriction enzyme
recognition sites from a DNA sequence. The recognition sites for
each restriction enzyme can be entered by hand from the keyboard,
but that is practical when only a few recognition sites are
scanned. The number of known restriction enzymes is quite large
and therefore the list of their names and recognition sites is
collected into a file. Two such files are provided with the
DrawMap program: The file ALL.ENZ contains most commercially
available restriction enzymes, with many isoschizomers
(recognizing the same sequence) omitted, however. The file
6BASE.ENZ contains a subset of the enzymes in ALL.ENZ, containing
those which recognize at least 6-base long sequences. The sources
for the enzyme files in this version of DrawMap are: Kessler, C
& Manta, V (1990) Gene 92:1-248 and Roberts, RJ (1990) Nucl.
Acids Res. 18:2331-2365.
    The enzyme files are most conveniently updated or edited into
subsets with any standard text editor. The characters 1-25 are
reserved for the enzymes name and 26-75 for the recognition
sequence. For how the alternate bases in the recognition sequence
are coded, please refer to Table III in the DNA SEQUENCE section.
Keep in mind that the search sequences do not have to correspond
to restriction enzymes, they can be anything the user needs. And
please do remember: Edit always only copies of the original .ENZ
files ! As an example, the file ALL.ENZ is listed below.


Aat2                    GACGTC
Acc1                    GTVWAC
Acc3                    TCCGGA
Acy1                    GPCGQC
Afl2                    CTTAAG
Afl3                    ACPQGT
Alu1                    AGCT
Alw1                    GGATC
AlwN1                   CAGNNNCTG
Apa1                    GGGCCC
ApaL1                   GTGCAC
Asn1                    ATTAAT
Asu1                    GGNCC
Asu2                    TTCGAA
Ava1                    CQCGPG
Ava2                    GGRCC
Ava3                    ATGCAT
Avr2                    CCTAGG
Bal1                    TGGCCA
BamH1                   GGATCC
Ban1                    GGQPCC
Ban2                    GPGCQC
Bbv1                    GCAGC
Bcl1                    TGATCA
Bgl1                    GCCNNNNNGGC
Bgl2                    AGATCT
Bsa1                    GGTCTC
BsaA1                   QACGTP
BsaB1                   GATNNNNATC
BsaJ1                   CCNNGG
Bsm1                    GAATGC
BsmA1                   GTCTC
BspH1                   TCATGA
BspM1                   ACCTGC
Bsr1                    ACTGG
BssH2                   GCGCGC
BstE2                   GGTNACC
BstN1                   CCRGG
BstX1                   CCANNNNNNTGG
Cfr10I                  PCCGGQ
Cla1                    ATCGAT
Dde1                    CTNAG
Dra1                    TTTAAA
Dra2                    PGGNCCQ
Dra3                    CACNNNGTG
Drd1                    GACNNNNNNGTC
Dsa1                    CCPQGG
Eae1                    QGGCCP
Ear1                    CTCTTC
Eco47III                AGCGCT
EcoN1                   CCTNNNNNAGG
EcoR1                   GAATTC
EcoR5                   GATATC
Esp1                    GCTNAGC
Fnu4H1                  GCNGC
FnuD2                   CGCG
Fok1                    GGATG
Hae2                    PGCGCQ
Hae3                    GGCC
Hga1                    GACGC
HgiA1                   GRGCRC
Hha1                    GCGC
Hinc2                   GTQPAC
Hind3                   AAGCTT
Hinf1                   GANTC
Hpa1                    GTTAAC
Hpa2                    CCGG
Hph1                    GGTGA
Kpn1                    GGTACC
Mae1                    CTAG
Mae2                    ACGT
Mae3                    GTNAC
Mbo2                    GAAGA
Mlu1                    ACGCGT
Mnl1                    CCTC
Mse1                    TTAA
Mst1                    TGCGCA
Nae1                    GCCGGC
Nar1                    GGCGCC
Nci1                    CCSGG
Nco1                    CCATGG
Nde1                    CATATG
Nhe1                    GCTAGC
Nla3                    CATG
Nla4                    GGNNCC
Not1                    GCGGCCGC
Nru1                    TCGCGA
Nsp1                    PCATGQ
NspB2                   GCSGC
PflM1                   CCANNNNNTGG
Ple1                    GAGTC
PmaC1                   CACGTG
PpuM1                   PGGRCCQ
Pst1                    CTGCAG
Pvu1                    CGATCG
Pvu2                    CAGCTG
Rsa1                    GTAC
Rsr2                    CGGRCCG
Sac1                    GAGCTC
Sac2                    CCGCGG
Sal1                    GTCGAC
Sau1                    CCTNAGG
Sau3A                   GATC
Sca1                    AGTACT
ScrF1                   CCNGG
SfaN1                   GATGC
Sfi1                    GGCCNNNNNNCCGG
Sma1                    CCCGGG
SnaB1                   TACGTA
Spe1                    ACTAGT
Sph1                    GCATGC
Spl1                    CGTACG
Ssp1                    AATATT
Stu1                    AGGCCT
Sty1                    CCRRGG
Taq1                    TCGA
Tth111I                 GACNNNGTC
Xba1                    TCTAGA
Xca1                    GTATAC
Xcm1                    CCANNNNNNNNNTGG
Xho1                    CTCGAG
Xho2                    PGATCQ
Xma3                    CGGCCG
Xmn1                    GAANNNNTTC



Appendix C

Modifying the DMDISP.TXT file


    Some modifications in the DMDISP.TXT file, the base of the
editing screen, may be very valuable for the user. This file,
however, is even more in the heart of DrawMap than the standard
and enzyme files described in appendixes A and B. Therefore, be
extremely careful in not scrambling it and always retain an
original copy in a safe place. The file contains some graphical
characters and therefore it may not be compatible with all text
editors.
    What you can do with the DMDISP.TXT file is to modify the
default data items in new maps. Typically, you may want the
comment screen to be, not empty, but have your name and address
in it automatically. You may also want to modify the basic map
components like character sizes so that they will always appear
in the nicer form in new maps. Note that the data in the file
DMDISP.TXT never affects the data in existing maps, only in new
ones.
    Not every map component can be predefined. Specifically, the
COMPOSITION OF THE PLASMID CIRCLE, the GENES and the SITES cannot
be given predetermined values. However, you can predetermine
strings or values for the FILENAME, PLASMID NAME and the SIZE.
That is more a curiosity, so let's start from the first real
thing, the FORM:
    The FORM determines how the map will be drawn: circular or
linear. Internally all maps are circular, so that for example the
coordinates 0 and SIZE are the same thing. If you want your maps
to be drawn linear by rule, enter "linear" in the FORM box, or
anything else than "circular".
    The LINE TYPES table contains data which you may need to
modify. For example, the number of lines in the "heavy" line type
may not be sufficient to give a solid line on your plotter and
you should increase it. You can also change the name of the LINE
TYPE, appearing on the right of the table. This, however, is not
really data, carried with each plasmid, but rather a comment on
the editing screen. That means that the change made will show
while editing old maps, too.
    The last line of the LINE TYPES table has a back-slash (\)
as its first character. This means that the rest of the lines,
up to the maximum of twenty, are copies of this line. (When you
move in the editing screen of DrawMap, the lines 6-20 exist
always in the memory. They are not shown unless their data is
different from 0-0-0. The first five lines show always.) If you
look at the codes on the right, you will see code 005 on this
row. It means that five lines in this table (named E04) was
explicitly written before the back-slashed template appears. This
may look a bit complicated, but it allows you to extend the list
of predefined line types: Insert, between LINE TYPEs 5 and 6,
copies of e.g. line 5 and edit their values into what you want,
including the comment on the right. Renumber the LINE TYPES and,
most importantly, modify the code (originally 005) to correspond
to the new number of lines before the back-slashed one.
    Going forward in the file, the COMPOSITION, GENES and SITES
are the tables where modifications of the DMDISP.TXT file have
no effect. The suppression list allows them again. Originally it
is set to draw everything except the box around the comments.
Maybe you want to have the plasmid boxed instead. If you want a
particular component to be drawn, write "  active  " in the box,
nicely with lower case letters and two leading and trailing
spaces. If you do not want a particular component drawn, write
in something else, e.g. "suppressed".
    In the PICTURE COMPONENTS, you can modify the right column
containing the default values. The left column is for the
plasmid's own data and not read from the DMDISP.TXT file. The new
maps get gets got getting their data directly from the default
values of this table. The modifications you make here show also
if old maps are edited. They do not affect the old map's data,
unless CTRL-D is pressed to reset a particular value for its
default.
    The last box is the COMMENT box where you can write your name
or something else you want to appear on all new maps. Note that
an eleventh line of the comment box (with the code 010) appears
to be available. However, it is not shown on the editing screen.
Still, do not remove it from the file since it tells DrawMap that
the maximum number of lines (10) was already shown.
    The last functional line of DMDISP.TXT is the line with the
text ----END. Do not remove or modify that. It tells DrawMap
where the file ends. What follows, is only comments. In the
original file it gives a short description of the structure.
    What was just described, was the modification of the data
which DrawMap has been designed to read from the DMDISP.TXT file
for new maps. However, there are more possibilities in tampering
with the file. The data tables are formed by the parts of the
file where the code at the right has the letter E followed by a
number. What is not data in the tables, written inside the boxes,
is comment text that you can modify at your will. Between the
tables are lines with the code I instead of E. They are
intervening lines between the tables and contain only comment
text that can be modified. Even more, you can add more
intervening lines, or delete away existing ones. For example, if
you would prefer different commenting or more elaborate help in
the editing screen, you can add it yourself.
    Finally, you may want to know about the lonely digit code at
the right hand side of the texts. That is a color code where 1
stands for green, 2 cyan, 3 blue and 9 a special mix: vertical
bars blue, text between them gray, and text after them green. (Do
not use code 9 except in tables, however!) Of course, you may
have changed the colors green, cyan, blue and gray to something
different in the SETUP section.
    The full listing of DMDISP.TXT follows. Compare it with the
listing of the editing screen shown in figure 6.
    Good luck and don't mess it !


 In this section you can establish or edit the coordinates according to    1I01 000
 which the circular plasmid map will be drawn. Although limited notes      1 I01 000
 are added among the data tables below, reference to the program manual    1 I01 000
 is recommended.                                                           1 I01 000
                                                                           1 I01 000
 For information concerning how to move around, press <F1>.                1 I01 000
                                                                           1 I01 000
 To exit, press <ESC>.                                                     1 I01 000
                                                                           1 I01 000
                                                                           1 I01 000
                                                                           1 I01 000
                                                                           1 I01 000
                                                                           1 I01 000
                                                                           1 I01 000
 FILENAME                                                                  2 I01 000
 ┌────────────┐                                                            3 I01 000
 │            │                                                            9 E01 000
 └────────────┘                                                            3 I02 000
                                                                           1 I02 000
                                                                           1 I02 000
 PLASMID NAME                                                              2 I02 000
 ┌────────────────────┐                                                    3 I02 000
 │                    │                                                    9 E02 000
 └────────────────────┘                                                    3 I03 000
                                                                           1 I03 000
                                                                           1 I03 000
 SIZE                          FORM                                        2 I03 000
 ┌──────┐                      ┌────────┐                                  3 I03 000
 │      │                      │circular│                                  9 E03 000
 └──────┘                      └────────┘                                  3 I04 000
                               Change with C or L                          1 I04 000
                                                                           1 I04 000
                                                                           1 I04 000
 LINE TYPES OF THE PLASMID CIRCLE                                          2 I04 000
  no thickness lines  pen                                                  2 I04 000
 ┌──┬─────────┬─────┬────┐                                                 3 I04 000
 │ 1│  0.000  │   1 │  1 │ single                                          9 E04 000
 │ 2│  0.020  │   3 │  1 │ heavy                                           9 E04 000
 │ 3│  0.030  │   2 │  1 │ double                                          9 E04 000
 │ 4│  0.100  │   2 │  1 │ broad double                                    9 E04 000
 │ 5│  0.000  │   0 │  0 │ user defined                                    9 E04 000
\│ 6│  0.000  │   0 │  0 │ user defined                                    9 E04 005
 └──┴─────────┴─────┴────┘                                                 3 I05 000
 In the table below, reference is made to these line types.                1 I05 000
                                                                           1 I05 000
                                                                           1 I05 000
 COMPOSITION OF THE PLASMID CIRCLE                                         2 I05 000
    from     to  type                                                      2 I05 000
 ┌───────┬───────┬──┐                                                      3 I05 000
 │     0 │  1000 │ 1│                                                      9 E05 000
 │       │       │  │                                                      9 E05 000
\│       │       │  │                                                      9 E05 002
 └───────┴───────┴──┘                                                      3 I06 000
 To add arrows to the line borders, press > or < for the forward and       1 I06 000
 the backward arrow. At contradiction, the arrow at the thicker line       1 I06 000
 dominates. CTRL-A removes an arrowhead.                                   1 I06 000
 Overlapping definitions are allowed here and the latest definition        1 I06 000
 overrides the others. To compose the overlaps, exit the cursor from       1 I06 000
 the table.                                                                1 I06 000
                                                                           1 I06 000
                                                                           1 I06 000
                                                                           1 I06 000
 GENES                                                                     2 I06 000
   from     to    D            name                                        2 I06 000
 ┌───────┬───────┬─┬──────────────────────────────┐                        3 I06 000
 │       │       │ │                              │                        9 E06 000
\│       │       │ │                              │                        9 E06 001
 └───────┴───────┴─┴──────────────────────────────┘                        3 I07 000
 Enter the genes in a clockwise direction irrespective of                  1 007 000
 their actual direction.                                                   1 007 000
 To add arrowheads to the ends of the genes, press > or <                  1 I07 000
 while staying in the coordinate box. CTRL-A removes an                    1 I07 000
 arrowhead.                                                                1 I07 000
 The D-box shows the direction of the gene name                            1 I07 000
 on the map. It is calculated as you exit the line if the                  1 I07 000
 D-box is empty. You can edit also the D-box.                              1 I07 000
                                                                           1 I07 000
                                                                           1 I07 000
 SITES                                                                     2 I07 000
 coordinate       name           type                                      2 I07 000
   ┌──────┬────────────────────┬──────┐                                    3 I07 000
   │      │                    │      │                                    9 E07 000
\  │      │                    │      │                                    9 E07 001
   └──────┴────────────────────┴──────┘                                    3 I08 000
   If the name box is left empty, the previous name is                     1 I08 000
   copied in the box.                                                      1 I08 000
   CTRL-T changes the site type (enzyme, by default).                      1 I08 000
                                                                           1 I08 000
                                                                           1 I08 000
 SUPPRESSION LIST                                                          2 I08 000
    status    component                                                    2 I08 000
 ┌──────────┐                                                              3 I08 000
 │  active  │ Draw a box around the map                                    9 E08 000
 │  active  │ Write the plasmid name                                       9 E08 000
 │  active  │ Write the plasmid size                                       9 E08 000
 │  active  │ Write the site coordinates                                   9 E08 000
 │  active  │ Write the site names                                         9 E08 000
 │  active  │ Draw the site marks                                          9 E08 000
 │  active  │ Write the gene names                                         9 E08 000
 │  active  │ Draw the gene arcs                                           9 E08 000
 │suppressed│ Draw a box around the comments                               9 E08 000
 │  active  │ Write the comments                                           9 E08 000
 └──────────┘                                                              3 I09 000
 Change status by CTRL-S                                                   1 I09 000
                                                                           1 I09 000
                                                                           1 I09 000
 PICTURE COMPONENTS                                                        2 I09 000
 current  default                                                          2 I09 000
  value    value   component                                               2 I09 000
 ┌───────┬───────┐                                                         3 I09 000
 │       │ 0.090 │ sites: character size  (y-comp)                         9 E09 000
 │       │ 1.00  │        character shape (x/y ratio)                      9 E09 000
 │       │ 0.070 │ genes: character size  (y-comp)                         9 E09 000
 │       │ 1.00  │        character shape (x/y ratio)                      9 E09 000
 │       │ 0.150 │ name:  character size  (y-comp)                         9 E09 000
 │       │ 0.67  │        character shape (x/y ratio)                      9 E09 000
 │       │ 0.20  │ length of the site mark                                 9 E09 000
 │       │    1  │ number of blanks after the longest enzyme name          9 E09 000
 │       │ 0.80  │ distance of the gene arcs from center                   9 E09 000
 │       │   50  │ angle of the gene arrows                                9 E09 000
 │       │   80  │ angle of the block arrows on the plasmid                9 E09 000
 │       │ 1.00  │ magnification  (max      )                              9 E09 000
 └───────┴───────┘                                                         3 I10 000
 Press CTRL-D to retain the default value.                                 1 I10 000
                                                                           1 I10 000
                                                                           1 I10 000
 COMMENTS                                                                  2 I10 000
 ┌────────────────────────────────────────────────────────────────────────┐3 I10 000
 │                                                                        │9 E10 000
 │                                                                        │9 E10 000
 │                                                                        │9 E10 000
 │                                                                        │9 E10 000
 │                                                                        │9 E10 000
 │                                                 University of Helsinki │9 E10 000
 │                                                 Department of Genetics │9 E10 000
 │                                                 Arkadiankatu 7         │9 E10 000
 │                                                 SF-OO1OO Helsinki      │9 E10 000
 │                                                 FINLAND                │9 E10 000
 │                                                                        │9 E10 010
 └────────────────────────────────────────────────────────────────────────┘3 I11 000
                                                                           1 I11 000
                                                                           1 I11 000
                                                                           1 I11 000
                                                                           1 I11 000
                                                                           1 I11 000
                                                                           1 I11 000
                                                                           1 I11 000
                                                                           1 I11 000
                                                                           1 I11 000
----END
THE USED PART OF THIS FILE ENDED TWO LINES AGO.
THE FILE IS AN IMAGE OF THE DISPLAY FOR EDITING MAP COORDINATES
FOR THE DRAWMAP PROGRAM.

THE STRUCTURE OF THIS FILE IS:

CHARACTER
        1   \ MEANS THAT THE LINE IS NOT SHOWN ON SCREEN
     1-75   CONTAINS THE TEXT FOR THE SCREEN
       76   GIVES THE COLOR OF THE LINE
       77   EMPTY
    78-80   TELLS WHAT PART OF THE DISPLAY THE LINE BELONGS TO
              -E MEANS ACTUAL DATA LINE
              -I MEANS COMMENT LINE
       81   EMPTY
    82-84   NONZERO AFTER A LINE WHICH CAN BE REPEATED ACCORDING TO
            A PROGRAM PARAMETER. TELLS THE PROGRAM HOW MANY LINES
            HAVE ALREADY BEEN USED IN THE BLOCK.


Appendix D

The structure of the .MAP files


    The plasmid map files (the .MAP files) need never to be
modified by hand when DrawMap is used. Still, they are easily
readable text files and their structure is described here. The
structure is closely related to the editing screen and is more
or less a listing of the contents of the editing boxes and
tables. The example map file listed here, PHTT172.MAP,
corresponds to the circular map shown in figure 7 and to the
editing screen shown in figure 6.
    The first line is a signature of the file and the DrawMap
program reads the version number from this line. The program can
always handle .MAP files of older versions, but encountering a
file made by a newer version of DrawMap causes an announcement.
Reading and comprehending will be tried anyway.
    The second line contains the plasmid name. Note that the file
name is not included in these lines so that renaming the .MAP
file with DOS is no problem. The next line contains plasmid size
and the tag C or L for circular or linear presentation of the
drawing. All the numbers are aligned and right justified. It is
necessary to keep them that way.
    Next follows the data of the LINE TYPES table. It is preceded
by the number 20, denoting that the next twenty lines will form
the LINE TYPES table. The first column of the table is multiplied
here by 1000, compared to the table in the editing screen.
    After LINE TYPES, the COMPOSITION table is presented, again
preceded by the number of lines belonging to this packet, this
time seven. The first three columns correspond to what you see
in the editing screen: form, to and type. The last one codes the
arrow heads, describing the left end arrow (i.e. at the from
coordinate ) in the following way:
1: arrow to the  left,  left type broader
2: arrow to the  left, right type broader
3: arrow to the right,  left type broader
4: arrow to the right, right type broader
Left refers here towards smaller coordinates and right towards
larger. Note that the code includes data of which side of the
border is broader and which in effect has the arrow protrusion
or indentation.
    The set of lines following describe the GENES, preceded by
number of lines. The first two columns correspond to the from and
to coordinates, the next two show the presence of arrowheads at
these coordinates (0: no, 1: yes), the one character column shows
the D or direction-of-name column and what remains is reserved
for the name of the gene. Next appear the SITES, lead by the
count of lines again. Between the coordinate and the enzyme name
is a column which indicates whether the site is an enzyme (e) or
a marker (m).
    In the rest of the file there are no number-of-lines
indicators, since the number is fixed in each case. The list of
FALSE and TRUE corresponds to the SUPPRESSION LIST (TRUE is
active, FALSE is suppressed). The numbers following the
suppression list describe the PICTURE COMPONENTS and the last ten
lines the COMMENTS.



Drawmap version 2.0 map file
pHTT172
      5923C
        20
         0         1         1
        20         3         1
        30         2         1
        80         2         2
       150         0         1
        20         3         3
         0         0         0
         0         0         0
         0         0         0
         0         0         0
         0         0         0
         0         0         0
         0         0         0
         0         0         0
         0         0         0
         0         0         0
         0         0         0
         0         0         0
         0         0         0
         0         0         0
         7
     -2336         0         1         0
         0      1180         4         0
      1180      1181         5         4
      1181      2200         2         0
      2200      3587         4         0
      3587      5923         1         0
      5923      7103         4         0
         3
      1234      2055         0         1-npt2
      3918      4755         0         1-amp
       592       592         0         0+P-stem
        10
         0eEcoR1
        12eBamH1
      1185eBcl1
      1431ePst1
      1464ePvu2
      2863ePst1
      3587eHind3
      3678ePvu2
      4194eSca1
      5743ePvu2
FALSE
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
TRUE
FALSE
FALSE
     0.090
      1.00
     0.090
      1.00
     0.150
      0.67
      0.20
      3.00
      0.80
     50.00
     80.00
      1.40
The npt2 containing BamH1-Hind3 fragment from tobacco TNT7#3 in pUC8.



                                                 Teemu Teeri
                                                 University of Helsinki
                                                 Department of Genetics
                                                 Arkadiankatu 7
                                                 SF-OO1OO Helsinki
                                                 FINLAND


Appendix E

The DrawMap character set


    The DrawMap character set follows the IBM extended character
set for the characters from SPACE (ASCII code 32) forwards. To
this, there are three exceptions: characters with codes 246, 249
and 250 are sacrificed for S, R and ■. The listing of the DrawMap
character set is (not on this version...) shown at the end of
this appendix together with their corresponding IBM set
characters and ASCII codes. You can see the three exceptions
there.
    Keyboards do not contain keys for all the special characters.
You can access them by pressing and holding down the ALT key and
simultaneously typing the characters' code on the numerical key
pad. When you release the ALT key, the character appears on
screen. Notice that the three DrawMap-specific characters appear
in their IBM form on screen - they are special only on drawn
maps.
    The character set is defined by the file DMCHARS. It is a
readable text file and simple enough for the user to make
modifications in. If you feel that the set is lacking a character
you would like to use, you can sacrifice more of the IBM
characters for your special purpose.
    The characters are based on a four by eight grid, shown on
the left. The letter A, for example, fits the grid as shown
below. If you dig into the DMCHARS file (pick it in a text editor
or just type TYPE DMCHARS), you will see rows of three digits
interrupted by rows of two digits. The two-digit rows are always
headings: they contain first the ASCII code of the character and
then the number of lines following belonging to the characters'
description. The description, the collection of three-digit
lines, is like a collection of imaginary pen strokes. The first
two digits define a point on the grid and the last whether the
imaginary pen should draw (1) or not (0) when moving there. The
definition of the character A, extracted from the file DMCHARS
is listed below. You can follow the pen movements on the grid
shown above.
 65  5
  0  0  0
  2  6  1
  4  0  1
  1  3  0
  3  3  1
    If you want to create a new character for DrawMap, make first
a copy of the grid. On the grid, by using straight lines from
point to point, design your new character or figure. Next write
down a code for the imaginary pen that would draw the new
character. You can draw it in any order, but since the maximum
number of lines is 30, jumping around should be rationalized at
least for complex characters. Count your lines and write the
heading: first the ASCII code you want to replace and then the
number of lines to follow.
    The next step is to insert your code in the DMCHARS file.
Pick the file in a text editor and search the corresponding ASCII
code and character definition. Now replace the lines describing
the character by your own. It is important to align your digits
as the other digits are aligned in the file. Equally important
is to remove all of the old code and write a correct heading
line. However, you are not limited to the size of the grid shown
above! Characters fitting in the grid will align nicely in
written text, all right, but you can use any coordinates between
-99 and 127. (In fact the special characters S and R already
extend beyond the grid.) For special purposes, it may be useful
to know that the consecutive characters in text have two blank
grid units between them (i.e., the spacing is 6 grid units). If
the maximum of 30 lines for pen code feels limiting, you can
compose the complex thing by a character pair, the latter
displaced left by 6 grid units !
    Finally, a reminder of good working practice: always save the
original DMCHARS file in a safe place. It is easy to make
disastrous mistakes in editing this file. You wouldn't want to
loose your characters, would you ?



Appendix F

Installation of DrawMap


    The DrawMap program is supplied on two 360K  5.25 inch floppy
disks. In order to run DrawMap, all of the files on these
diskettes (except the file INSTALL.BAT) should be copied on one
hard disk or larger diskette, in a directory named \DRAWMAP. A
hard disk is recommended because of its superior speed.
Alternatively, DrawMap can be supplied on a single 1.44M  3.5
inch diskette from which it can be run directly. This diskette,
too, contains the installation program for installation on hard
disk.
    The DrawMap diskette 1 contains an automatic installation
program. When you run it, give both the source and the
destination disk as program parameters. E.g., if you want to
install DrawMap on drive C and the DrawMap diskette 1 is in drive
A, type
INSTALL A: C:
Also, if you want to update your DrawMap with a newer version,
you can run the installation program. 500 K of space should be
free on your disk before you install DrawMap. The program needs
the disk also as working space. Some 200K free before starting
DrawMap should be safe for most purposes. (It really depends on
how huge sequences you analyze with what incredible number of
enzymes in the DNA SEQUENCE section).
    DrawMap is written in Turbo Pascal version 5.0 and it is
designed to run in an IBM PC compatible computer. The graphics
displays supported are the CGA, EGA, VGA and the Hercules
displays. The support of the displays requires the corresponding
.BGI file to be found in the \DRAWMAP directory. However, you can
dispose of the ones you do not need.
    DrawMap needs a minimum of 300 K free ram memory to run. Any
extra ram, up to 640K, can be used to speed up matrix printer
drivers and to analyze an even larger DNA sequence in the DNA
SEQUENCE section. If you have extended or expanded memory in
excess of the 640K and you could configure it as a virtual disk,
DrawMap will run even faster when loaded there. Be careful not
to save your map files on the virtual disk since it is volatile
and the data is lost when the computer is switched off.
    DrawMap needs to be started from the directory \DRAWMAP. This
does not limit the use of the program in a personal way by
different people in the lab. It is very convenient to have
personal DOS batch files to start the program and automatically
to change the directory. These small files are most easily typed
directly from the keyboard, e.g.:

copy con DMPETRI.BAT
cd \drawmap
drawmap \petri\maps
CTRL-Z

The first line tells DOS to copy from the console (keyboard) a
file named DMPETRI.BAT. The next two lines go into the file and
the last, CTRL-Z, finishes the copying. Every time DMPETRI is
called, the directory will automatically be changed to \DRAWMAP,
DrawMap will be started and it will, as the first thing, change
the directory to where Petri has his maps saved. Also, if you run
DrawMap from a virtual disk, it may be a good idea to start it
with a similar type of batch file which will cause automatic
saving of the map files on a physical disk.







Contact address:
                           Teemu Teeri
                           Institute of Biotechnology
                           University of Helsinki
                           Karvaamokuja 3
                           SF-00380 Helsinki
                           FINLAND
                           tel.  INT-358-0-434 6032
                           fax. INT-358-0-434 6046
                           E-mail: [e-mail]
                                   [e-mail]