volume 12 Number 1 1984 Nucleic A c i d s Research

PLASMAP: an interactive computational tool for storage, retrieval and device-independent graphic
display of conventional restriction maps

Barry N.Stone 1 *, Gloria L.Griesinger1 and Joseph L.Modelevsky2 +

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'Scientific Information Systems, 2Moleeular and Cell Biology Research, Lilly Research Laboratories,
Eli Lilly and Co., Indianapolis, IN 46285, USA

Received 12 August 1983

ABSTRACT

We describe an i n t e r a c t i v e computational t o o l , PLASMAP, which allows the

user to e l e c t r o n i c a l l y s t o r e , r e t r i e v e , and display c i r c u l a r r e s t r i c t i o n
maps. PLASMAP permits users to construct l i b r a r i e s of plasmid r e s t r i c t i o n
maps as a set of f i l e s which may be edited in the laboratory at any time. The
display feature of PLASMAP quickly generates device-independent,
a r t i s t - q u a l i t y , f u l l - c o l o r or monchrome, hard copies or CRT screens of
complex, conventional c i r c u l a r r e s t r i c t i o n maps.

INTRODUCTION
The circular restriction map is a conventional display for the
communciation of plasmid genetic information. Circular restriction maps can
contain a large amount of information in a single display: for example, dozens
of restriction sites and several genetic markers, plus supporting
information. Such maps often are the most efficient means of communicating
descriptions of plasmid constructions and derivatives. Conventional circular
restriction maps do not readily lend themselves to computerized display,
however.
To address this application, we have developed the computational tool,
PLASMAP. PLASMAP permits electronic storage, retrieval and display of
circular restriction maps and supporting information, and provides all the
benefits associated with computerized information management. Data files
containing map information may be readily created, edited, shared, and
transferred using system facilities and/or specialized programs.
In application at Lilly Research Laboratories, PLASMAP is a single
integrated component of the Eli Lilly and Company DNA Computing Environment
(DNACE). In this paper, our discussion will focus on PLASMAP as a stand-alone
module.

© IRL Press Limited, Oxford, England. 465

Nucleic Acids Research

MATERIALS AND METHODS

Hardware
PLASMAP has been implemented on a VAX 11/780 with VMS version 3.2
operating system. Data-file input may be made from a variety of alpha-numeric
terminals. Displays may be supported on a wide variety of color or monochrome
graphics devices (CRTs, printers, plotters).

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Software
PLASMAP is programmed in VAX-11 FORTRAN (FORTRAN 77) under VAX/VMS.
PLASMAP uses only character-string input and character and numeric output;
therefore, PLASMAP should be easy to rewrite in another language. PLASMAP
program structure is diagrammed in figure 1.
Maps are stored as ASCII data files which may be constructed interactively
in PLASMAP, with any system editor or as output from other programs. Numeric
fields are read in free format and can be preceded, separated or followed by
any number of spaces, commas or tabs. PLASMAP data file format is summarized
in Table 1. Graphic displays are driven by TEMPLATE version 3.0, a product of
MEGATEK, Inc.

RESULTS
PLASMAP information files (data files) are simple tables containing the
following information: a map title; the total number of bases in the plasmid;
the number of restriction sites to be displayed; the names and locations of
restriction sites to be displayed; the names, locations and orientation of
stored landmarks; and up to 10 lines of descriptive text. The structure of
the information file is checked when read by PLASMAP; the user is informed of
any format errors.
PLASMAP information files may be constructed interactively in PLASMAP or
may be constructed using any system file editor at any alpha-numeric computer
terminal. In DNACE, we routinely use VT52, VT100, VT131 and equivalent
terminals as input devices. PLASMAP displays, driven by TEMPLATE, may be
supported by a wide variety of graphics devices: printers, plotters, CRTs. In
DNACE, PLASMAP display is most commonly linked to a VERSATEC electrostatic
plotter, Hewlett-Packard 8-pen plotters, Retrographics VT640 CRTs, or
IDSystems ID1OOV CRTs.
PLASMAP plots a conventional map of a plasmid. PLASMAP tests and
automatically compensates for overlapping sites and overlapping markers and
provides for variable "white space" around the components of the display.
Restriction sites are displayed as tics with labels on a circle. Enzymes

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PLASMAP program structure.

Figure 1.
Nucleic Acids Research

Table 1 . PLASMAP data file format.

Line No Contents
1 Map Title
2 Number bases in plasmid

3 Number of restriction sites = m

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2+ 2*i Label of Restriction site (i)
3+ 2*i Location (base number) of Restriction site (i)

Repeat for i = l,2,3,....m

4+ 2m Number of landmarks = n

3+ 2m + 2j Name of landmark (j)

4+ 2m + 2j Starting and ending locations, arrow direction flag,

for landmark (j)

Repeat for j = 1,2,....n

5+ 2m + 2n Number of lines of text = p

+
5+ 2m + 2n k Text line (k)

Repeat for k = 1,2,....p

Total lines in file = 5 + 2m + 2n + p

sharing a cut site are separated by "/" marks; sites close to each other are
separated by shifting the labels, then connecting them to their tic marks.
Landmarks (e.g., genetic markers) are displayed as labels inside the circle
with directional arcs delimiting the extent and orientation of the landmark.
Overlapping landmarks are separated by altering the radii of the arcs which
delimit the landmarks. Directionality of landmarks is indicated by arrowheads
on the end of the delimiting arc.
Descriptive text can contain up to 10 lines for a display of standard page
size. Because display parameters are automatically determined by PLASMAP, the
user need only concern himself with entering the correct map information into
the PLASMAP information file.
As shown in figures 2 and 3, a sophisticated restriction map display is

468
 Nucleic Acids Research

PSEUDO pBR322 Derivative

4363
26
EcoRI
4363
Clal
23
Hlndlll
29
BanHI
375
SphI
561

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AccI
650
Ace I
2245
Hindi
650
1000
1000
Hindi
3906
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650
2000
2000
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938
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971
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1424
4000
4000
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J443
PvuII
2065
3000
3000
Tthllll
22)8
Snal
2245
HgiEII
2294
HglEII
3055
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3734
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3845
6
Px
2000 2200
RBS
2200 2250
Gene X
2251 3000
Clone Here
3610 36] !>
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Tet
40 1
10
S a n p l e P L A S M A P data file and d i s p l a y . A simple a l p h a - n u m e r i c table Js c o n v e r t e d
Into a g r a p h i c display of a c o n v e n t i o n a l , i n f o r m n t i o n - d e n s e , circular
restriction nap. T M 3 map Includes locations of several known restriction
enzyme recognition sequences occuring two or fewer times in pRR322DNA. The
positions of the tetracycllne and ampiclllln resistance genes; samples of
overlapping landaarks and a pseudo cloned expression unit (Px, promoter X;
RBS, rlbosone binding site; Gene X) are also indicated. Plotted on Hewlett-
Packard 7220 plotter.
Restriction sites from Sutcllffe, J.G., Cold Spring Harbor Symposium (1979) 43,
77-90.

gure 2. A PLASMAP information file.

469
Nucleic Acids Research

PSEUDO pBR322 Derivative

4000 BafflHI
HTncI 1
Rrul Sphl
Ace I/Hind I/So I I

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HgiElI /I I 200°
Accl/Snal P*"11
Tth11 1 I
Sample PLASMAP data file and display. A simple alpha-numeric table Is converted
Into o graphic display of a conventional. Information-dense, circular
restriction map. This map Includes locations of several known restriction
enzyme recognition sequences occurlng two or fewer times In pBR322DNA. The
positions of the totracyclino and amplclI I In resistance genes: samples of
overlapping landmarks and a pseudo cloned expression unit (Px, promoter X;
RBS, rlbosome binding site; Gene X) ore also Indicated. Plotted on Hewlett-
Packard 7220 plotter.
Restriction sites from Sutcllffe, J.G., Cold Spring Harbor Symposium (1979) 43,
77-90.

Figure 3. Restriction map display generated by PLASMAP from a simple

PLASMAP information file.

generated from a simple PLASMAP information file. When linked to color

graphics display hardware, color coding of information is superimposed on the
line drawing; for example, titles and plasmid DNA are displayed in black or
white (depending on the display device), restriction sites are displayed in
blue, landmarks are displayed in green, supporting information is displayed in
red. Color coding may be adapted to any convention.
PLASMAP runs rapidly. The overall interactive and display response time
is highly dependent upon the host computer and its computational load. In
ONACE, on a shared VAX 11/780, screens are painted instantly at 9600 baud or
greater. At 1200 and 2400 baud, the most complex maps take about 30 seconds
to complete.
PLASMAP may be interfaced with operators which edit PLASMAP data files to
allow simulations of insertions, deletions, etc. The output from programs

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 Nucleic Acids Research

which calculate restriction maps may be formatted for use as PLASMAP data
files. The graphic display, driven by TEMPLATE, may be manipulated to provide
for rotations, magnifications, etc.

DISCUSSION
Computational tools designed to store, retrieve and display restriction

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maps have been described previously (1,2,3). In general, these tools make use
of linear displays or circular displays which do not resemble the maps
commonly drawn by the molecular biologist. PLASMAP provides electronic
storage and retrieval capabilities for restriction map information and
provides device-independent display of conventional circular restriction maps.
PLASMAP data files are essentially electronic file cards containing the
information composing a complex restriction map. The information files are
structured simply and read in free format, facilitating creation of map files
by the user. Site names with locations may be entered in any order. Landmark
names with locations and orientations may also be entered in any order.
Descriptive text may be included within the data file.
Resultant restriction map displays are similar to those found in most
publications. PLASMAP is capable of displaying virtually any map; limits are
imposed by the font size and the density of information in a sector of the
map. The practical limits of PLASMAP display correspond to the practical
limits one would apply to the amount of information condensed into a single
map.
The simple format for PLASMAP information files facilitates interfacing
with most restriction mapping programs: the trapping of output and formatting
into retrievable PLASMAP files should be a simple programming task. The
development of map manipulating programs is an independent task, and may be
implemented as PLASMAP information file editors.

•Current address: Texas Instruments, Dallas, TX 79266, USA

+
To whom communications should be addressed

REFERENCES
1. Lilley, D.M.J. (1982) Nucleic Acids Research 10 (1), 19-26.
2. Pearson, W.R. (1982) Nucleic Acids Research 10 (1), 217-228.
3. Bach, R., P. Friedland, D.L. Brutlag and L. Kedes (1982) Nucleic
Acids Research 10 (1), 295-304.

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