The objective
is to automate all the various methods of
sequence exploration around a central database. The information agents
access other web sites or programs installed in the UTHSCSA bioinformatics
center. The object is not to reinvent the wheel, but to harness many
wheels.
The following link allows access at a non graphics level
to any information currently compiled in the database supporting the ongoing
analysis of phageD. This includes data deposited from a growing number
of information agents deployed in the project, as well as notes, comments,
and literature links recorded as the investigators pursue a higher level
understanding of the genome.
PhageD
database.
Database specifics:
-
Schema
supports mixed controlled language and non controlled language data.
-
Access: Perl DBI or
apache CGI -> Perl DBI.
Information agents: Perl
LWP.
Display: Public interface through CGI gateway.
Editing: Private forms-based html interface secured by
htaccess and customized database security layer.
Graphics: BioPerl,
Bio::Graphics
& Generic Genome Browser.
The graphics capabilites available in these packages
have thus far barely been touched in this project, but are a priority for
the future. The 2 phage D figures below in this presentation were
created using Bio::Graphics, at a tiny fraction of the time it would have
taken to draw them with powerpoint. The Generic Genome Browser, once
implemented here, will allow web access to graphics created on the fly
to exemplify various currently difficult to visualize relationships among
different phage genomes.
Partial
compendium of scripts.