Plant Genome II Conference
Town & Country Conference Center, San Diego, CA, January, 1994.
PG-II: THE EXPRESSED GENE ANATOMY (EGAD) AND SEQUENCES, SOURCES, TAXA
(SST) DATABASES: RATED BIOLOGICAL DATABASES TO SUPPORT RESEARCH
IN GENE DISCOVERY AND EVOLUTION
THE EXPRESSED GENE ANATOMY (EGAD) AND SEQUENCES, SOURCES, TAXA
(SST) DATABASES: RATED BIOLOGICAL DATABASES TO SUPPORT RESEARCH
IN GENE DISCOVERY AND EVOLUTION.
Carol Bult, Judith Blake, Anthony Kerlavage, Anna Glodek, Will
FitzHugh, Owen White, Granger Sutton, Lisa FitzGerald, Man-Wai
Chiu, Mark Adams, Rebecca Clayton, J. Craig Venter, and Chris
Fields, The Institute for Genomic Research (TIGR), Gaithersburg,
Maryland 20878.
We have developed two integrated, curated biological
databases, EGAD and SST. EGAD is designed to represent genes
with multiple transcripts, each of which may have a different
cellular role in each tissue and at each developmental stage that
it is expressed. SST integrates DNA and protein sequence data
with specimen, collection and taxonomic information. It is
intended to document the use of specimens from curated museum
collections in comparative molecular analyses and to facilitate
the proper documentation of all taxa used in molecular studies.
SST interfaces directly with EGAD and employs EGAD's
representation of DNA and protein sequences, multiple sequence
alignments, and trees. SST provides taxonomic representation
directly to EGAD and supports the representation of allelic
differences in EGAD. Together, EGAD and SST support research
efforts in gene discovery, molecular systematics, and
population-level genetic diversity. Both databases are
implemented using the SYBASE relational database management
system and are linked to our Expressed Sequence Tag Database
(ESTDB)1 through triggers and shared user interfaces.
SST and EGAD are being developed as publicly-accessible
resources as part of a federated system of interoperable
biological databases. Inquiries concerning test site access to
EGAD and SST should be directed to Dr. Anthony Kerlavage
(arkerlav@tigr.org).
1 Kerlavage et al., (1993). Proc. Hawaii Int. Conf. on System
Science. IEEE Computer Society Press, pp. 585-594.
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