Announcing: Additions to the BCM Search Launcher

Pamela Culpepper culpep at bcm.tmc.edu
Mon Jun 23 15:45:56 EST 1997


The BCM Search Launcher organizes and simplifies molecular
biology-related search and analysis services available on the WWW. It
provides a single point-of-entry for related services, for example, a
single page for launching nucleic acid sequence searches using standard
parameters. 

Updated Annotated Domains Database for BEAUTY

The Annotated Domains Database used with BEAUTY and
BEAUTY-X searches has been updated as of June 23, 1997. Annotations
are included from Entrez database entries up to June 13, 1997, PRINTS
version 16.0, PROSITE version 2.1.4, and BLOCKS version 9.3. This
updated database contains 194,632 sequences with 519,446 annotations,
compared to the previous edition of this database (Entrez version 20)
which contained 364,367 annotations. 

BEAUTY and BEAUTY-X searches of the non-redundant protein
sequence database, which present the annotations in the Annotated
Domains Database, are available from the "BCM Search Launcher"
Web pages http://gc.bcm.tmc.edu:8088/search-launcher/launcher.html
at the Human Genome Sequencing Center, Baylor College of Medicine. 

WU-BLAST2 with BEAUTY

WU-BLAST2, the new version of BLAST from Warren Gish which
includes gapped alignments is now available from the EMBL server via
the Protein Search Page and the Nucleic Acid Sequence Search page.
Both BLASTP and BLASTX versions include BEAUTY
Post-Processing. BEAUTY Post Processing adds additional information
including 1) a figure which summarizes the locations of the BLAST hits
and any Prosite hits with respect to the Query sequence; 2) figures
which show the locations of the BLAST hits and any Annotated domains
found in the Annotated Domains Database (announced above) with
respect to the database sequences; and 3) links to related databases.
All of this makes it much easier to analyze sequence database search
results.

GenBank formatted sequence file retrieval

The latest versions of the Search Launcher Batch Client (2.5 and
greater) allow sequence files to be retrieved from the NCBI's Entrez
server in GenBank format or Fasta format. Files of lists of sequence ID
numbers (either gi numbers or accession numbers) can be submitted via
the Batch Client to have each sequence file retrieved and stored
automatically to a separate file in the users directory.

The Search Launcher Batch Client is a Unix or Macintosh application
which will read-in multiple input files, perform a specified search on
each sequence (one at a time), then store the result files on the user's
system as individual files. This processing occurs in the background, so
the user does not need to wait for the search to complete to continue
with other work or to log-off a public terminal. 


Kim Worley, Ph.D.
Human Genome Sequencing Center
Department of Molecular and Human Genetics and W.M. Keck Center
for Computational Biology
Baylor College of Medicine, Houston, TX 77030 USA

sl-help at bcm.tmc.edu; 713-798-8292; FAX: 713-798-5386






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