clark@mshri.utoronto.ca (08/07/90)
Here is the abstract for the poster that I presented at the Fairfax
BioMatrix meeting last month:
A SIMPLIFIED INTERFACE FOR DATABASE SEARCHING WITH THE GCG PROGRAMS
Stephen Clark
Samuel Lunenfeld Research Institute
Mount Sinai Hospital, 600 University Avenue
Toronto, Ontario, Canada M5G 1X5
clark@mshri.utoronto.ca (Internet)
clark@utoroci (Netnorth/Bitnet)
The Genetics Computer Group (GCG) package, running in the VAX/VMS
environment, contains a number of programs to aid the molecular biologist in
sequence entry and analysis. The user interface is designed to provide maximum
flexibility through extensive use of command line switches. Unfortunately,
inexperienced computer users find this reliance on command line switches very
difficult to learn. The problem is compounded because most people use the
programs only occasionally and forget how they are run between sessions.
Especially problematic are the programs for searching the databases. They
should be run in batch mode because of the extensive CPU times involved (often
several hours), but there is no capability built into the GCG programs to do
this automatically. To help overcome some of these problems, I have written
DCL command procedure shells for CPU-intensive programs. These shells use a
menu-driven interface to query the user about the available options and
construct a command file that is automatically submitted to the batch queue,
thus enabling people who are unfamiliar with command line options, text
editors and batch processes to carry out a database search on their own. All
user responses are checked for errors as rigorously as possible. Shells are
available for Fasta, Tfasta, Wordsearch/Segments, Find and Strings. Other
shells (Famail and Dbmail) construct and send messages to the GenBank Fasta
and sequence retrieval email servers via Internet. Finally, there is a shell
to facilitate multiple Compare/Dotplot analyses with various levels of
stringency and window- or word-size. These command procedures are freely
available to anyone who would like to use them.