Worm Breeder's Gazette 11(1): 13

These abstracts should not be cited in bibliographies. Material contained herein should be treated as personal communication and should be cited as such only with the consent of the author.

gm2 Automated DNA sequence analysis system available

Chris Fields and Cari Soderlund

A prototype automated DNA sequence analysis system, gm2 is available 
to laboratories interested in serving as external test sites.  gm2 
consists of a set of pattern recognition and statistical analysis 
modules, together with a geometric modeling system.  It accepts as 
input a DNA sequence, consensus matrices for locating splice sites, 
translational start sites, and polyadenylation sites, match-quality 
cutoff values for consensus searches, and base frequency and codon 
usage standards for coding regions and introns.  It produces as output 
schematic models of the possible genes contained in the sequence that 
show the locations of the coding sequences, introns, and control 
signals; it also produces translations of each of the gene models into 
amino acid sequences.  The current version of gm2 generates all 
possible models of the gene content of a sequence that are consistent 
with the input parameters.  It is capable of analyzing sequences 
containing partial genes or multiple genes as well as sequences 
containing a single complete gene.  
gm2 is implemented entirely in C.  It employs a simple, prompt-
driven user interface; it can also accept input from a file.  It 
prints output to ASCII files.  gm2 can be run from a conventional text-
only terminal.  The system has been tested on Sun 3 and Sun 4 
workstations.  It will run on a Sun 3/50 with 4 Mb memory; a larger 
memory improves performance.  The system has been tested on a number 
of C.  elegans sequences in the 10 kb size range, and on composite 
sequences of up to 40 kb.  Complete and correct models of multi-exon 
genes, e.g.  myo-2 and unc-15, can be generated on a Sun 3 in run 
times ranging from less than 1 minute to roughly 30 min, depending on 
the search parameters used.  Runs on the Sun 4 are approximately four 
times faster.  
gm2 is available to university or other nonprofit laboratories, 
under the condition that they do not redistribute the software.  Users 
of the software will be asked to supply us with results of running gm2,
descriptions of problems that are encountered and suggestions for 
improvements.  Source code and documentation for gm2, and for 
Paper [wbg11.1p11]
Abstract [wbg11.1p11]

LongText [wbg11.1p11]
The CGC produces several different kinds of reference material for C.
elegans researchers in addition to providing nematode strains.  The 
following list describes the various items, the formats in which they 
are available and the date of the last version.  Text files on 
computer diskettes are organized very simply and can easily be used 
with dBase and word processor programs on a variety of microcomputers. 
The information in the computer files is updated weekly or monthly.  
Paper lists typically order information in a way that reduces the need 
to have it on a computer and they are updated annually or biannually.
All items are available on request.  Letters on departmental 
letterhead should be addressed to Mark Edgley at the CGC (see address 
in the subscriber list at the back of this issue).  Requests for 
computer text files must be accompanied by appropriate blank diskettes 
and information about the system and programs with which the data will 
be used (call Mark to find out the current size of each file).  All 
disk files come with a description of data organization and some brief 
instructions for use.  Paper lists may temporarily be unavailable if 
we have run out of copies and an update is in process.
Strain List:  All strains available from the CGC, giving strain name 
and genotype.  The paper version is automatically sent to every 
laboratory with CGC strain and allele designations.  It contains 
strains in order by genotype and the disk version contains them in 
order by strain name.  Last paper version: March, 1988.  Updates 
appear regularly in the WBG.
Bibliography:  All articles and book chapters on C.  elegans and C.  
briggsae from 1866 through the present.  The paper version (also 
automatically sent to all CGC labs) comes in two parts.  The first 
covers 1866 through 1985 and the second covers everything since 1985.  
The first part is not updated, but the smaller second part is updated 
biannually.  When the second part is as large as the first, a single 
list will again be generated.  Each part is composed of three 
sections: (1) the complete list in order by first author; (2) an 
abbreviated list in order by CGC key number; and (3) articles grouped 
by keyword.  The disk version contains articles in order by key number,
first author or journal (specify when you ask for it; the default is 
key number order).  Last paper version: March, 1988.  Updates appear 
regularly in the WBG.
Map Data:  All genetic mapping crosses considered in generating the 
C.  elegans genetic map.  The paper version is now only available as a 
special request item to laboratories doing genetic mapping, since it 
is too expensive to produce and mail routinely to a large number of 
laboratories (see the blurb in the Announcements section of this 
Gazette).  The printout is in three sections:  (1) Two-factor distance 
data; (2) deficiency/duplication complementation data; and (3) multi-
factor ordering data.  In each section, the entries are ordered by 
gene or rearrangement name.  The disk version contains entries in 
order by cross number.  Last paper version: June, 1988 update.  The 
disk files are updated during each map revision and are available 
shortly after the revision is published.
Map Drawing:  The computer drawing files for all genetic map 
sections are available for use on your own system.  The drawing is 
produced using the program 'Designer' (Micrografx, Inc., Richardson, 
Texas), which runs under Microsoft Windows on IBM-compatible 
microcomputers, with the sections formatted for printing on an Apple 
LaserWriter Plus (other printers may not have available the line 
widths and fonts we use).  You have to supply your own copy of 
Designer or other program that can read its drawing files.  Conversion 
programs are available from Micrografx to make the drawings usable in 
Autocad, PageMaker, Harvard Graphics, Ventura Publisher, Freelance, 
Draw Plus, Graph Plus, WordPerfect and PC Paintbrush.  These 
conversions are not perfect; some print attributes and image 
definition may be lost in translation and some programs do not allow 
editing.  Generally, the more sophisticated the program, the better 
the quality of the converted image.  The people at Micrografx are 
working on a program to convert drawings to Macintosh formats, but it 
is not yet available.  We have used Macintosh Freehand to open and 
print chromosome sections, but were not able to use it for editing.  
Last version: May, 1989, except for the left end of LG III, which is 
included with this Gazette.
WBG Subscribers:  The complete list of subscribers with addresses, 
phone numbers, FAX numbers and BITNET addresses is printed in the 
first issue of each volume of the Gazette and updates to the list 
appear in each subsequent issue.  The list is available as a computer 
disk file with the entries in order by last name.
WBG Tables of:  The Tables of Contents of most WBG issues (back to 
the first one) are available on diskette as rather crude, and in 
places, incomplete text files.  They include titles, authors, volume 
and issue numbers and page numbers.
Films:  The CGC owns two short 16mm films on C.  elegans that are 
available for loan.  The first is the Encyclopaedia Britannica film 
'Nematode', an 11-minute introduction to worm behavior and mutants 
using dictionary entries, music and toys for illustration.  The second 
is 'Embryonic Development of the Nematode Caenorhabditis 
nstitut f r den Wissenschaftlichen Film, also 
about 11-minutes long.  It is narrated time-lapse Nomarski photography 
of a developing embryo from fertilization through hatching, with a 
computer reconstruction of the embryo that rotates about its 
longitudinal axis to show relative positions of the nuclei.  Requests 
should be made well in advance of the date you want the films (one 
month is good), and it's a good idea to call first to make sure they 
are not already out on loan.