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CILIATEMOLBIO-L  May 2005

CILIATEMOLBIO-L May 2005

Subject:

TGD Gene Annotations and Genome Browser

From:

Nick Stover <[log in to unmask]>

Date:

Mon, 2 May 2005 17:00:36 -0700

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (52 lines)

Dear Ciliate Researchers,

Tetrahymena Genome Database (www.ciliate.org) now provides the TIGR
preliminary gene set with annotations, a graphical viewer, and much
more.  This is a major enhancement of the database information and
software.

Automatic annotations for each of the preliminary macronuclear protein
coding gene models predicted by TIGR are available.  RNA gene
predictions are also provided.  Top BLASTP hits, domain predictions,
and Gene Ontology (GO) annotations have been determined and are
displayed for each gene.  These annotations are all keyword searchable
- simply enter the name of the gene, homolog, domain, or GO term you
are interested in into the Quick Search box found on any TGD page.  We
have also added datasets containing TIGR’s preliminary gene models to
the TGD BLAST/BLAT server, to allow direct searching of the coding or
hypothetical protein sequences. The BLAST/BLAT resource has been
enhanced to provide hyperlinks to the TGD database and/or the TGD
GBrowse viewer from the search results.

Using the published literature, TGD curators have prepared descriptions
for each of the ~200 T. thermophila macronuclear genes that have been
deposited in the public sequence databases.  These descriptions, plus
links to literature describing these genes, are displayed above the
corresponding preliminary gene models determined by TIGR.  To see
examples of this layout, try searching for the name of a known gene,
like PDD1 or DYH2.

The preliminary protein and predicted RNA genes from the TIGR
macronuclear genomic sequence can now be viewed using GBrowse, a
popular genome display tool developed as part of the GMOD project
(http://www.gmod.org).  Click on the Genome Browser image shown on each
gene page to explore that gene's local area, or go directly to the TGD
GBrowse (http://db.ciliate.org/cgi-bin/gbrowse/tt-genomic) to search
the genome for gene names, descriptions, or even short nucleotide
sequences.  Use the zoom in/out and left/right panning features to home
in on your region of interest, then use the pulldown menu below the
figure to retrieve the sequence of that area.

We hope these new features provide you useful information for your
research and teaching.  We are eager to answer your questions about the
information and the tools we’ve provided.  Please email your questions
and comments to [log in to unmask]

Happy gene hunting!

The Staff at TGD
http://www.ciliate.org

*TGD is funded by the NIH as part of the Tetrahymena Genome Sequencing
Project and is supported by NIH and NSF grants to Jonathan Eisen at
TIGR.*

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