NETWORK SERVER FOR ELECTRONIC GENETIC ANALYSIS

Project: Research project

Project Details

Description

For many genetic loci, the rapid accumulation of sequence data from
several species, along with detailed functional analyses, has produced a
ponderous data set that is challenging, if not impossible, for individual
investigators to fully assimilate. We propose to develop a prototype
database of sequence alignments and experimental results for the beta-like
globin gene cluster of mammals. This data repository is intended to help
the international community of scientists studying globin genes to plan
experiments, to design models and, ultimately, to understand regulation of
those genes. The resource will be developed for mammalian beta-like
globin gene clusters because they have been thoroughly sequenced for
several species and extensive functional data are available. Moreover,
the approaches and software developed for this project will be applicable
to other sequence-analysis problems, and the prototype developed here will
be applicable to any locus for which extensive sequence and functional
data are available from several species.

We recently developed a program that can simultaneously align a few very
long sequences. An e-mail server was then established to deliver any
requested portion of the alignment, annotated to indicate highly-conserved
regions and known sequence features. This proposal seeks support to
develop an interactive Globin Gene Server on the Internet to provide
access to and analysis of both the alignments and experimental data. We
are currently refining a data model and a collection of tools to capture
and display the wealth of pertinent experimental data. Implementation of
these tools will allow the user to view the results of the simultaneous
alignment of sequences (conserved sequence blocks) in register with the
experimental data, thus providing an integrated view of the gene cluster
in a flexible, interactive format. This integrated view of both
alignments and experimental data in register, which we call electronic
genetic analysis, is a unique feature of this database. Future
developments will include tools to search the Transcription Factor
Database for matches to the consensus for conserved blocks, provide
alternative alignments, produce summary views of the database in an
interactive manner, support batch queries in classic database query
languages, and automatically detect database inconsistencies. To best
serve the needs of our potential user community, this information is being
made available via World-Wide Web, which is an interactive, graphically
oriented environment available over the Internet.
StatusFinished
Effective start/end date8/1/957/31/96

Funding

  • U.S. National Library of Medicine

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