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CILIATEMOLBIO-L  June 2005

CILIATEMOLBIO-L June 2005

Subject:

Preliminary Gene Name Updates at TGD

From:

Nick Stover <[log in to unmask]>

Date:

Thu, 9 Jun 2005 20:36:51 -0700

Content-Type:

TEXT/PLAIN

Parts/Attachments:

Parts/Attachments

TEXT/PLAIN (37 lines)

Dear Ciliate Researchers,

As part of the data synchronization effort between TIGR and TGD, we
have updated the names used to identify the preliminary gene models at
our site to match those shown at TIGR. The "PreTt" names used to
identify these gene models at TGD are still stored here and are shown
in the "Alias" field for each preliminary gene. These names can still
be used to search for your genes of interest.  We will soon be
providing a link from each gene's page at TGD to its corresponding gene
page at TIGR.

As a reminder, these gene models are preliminary and have not been
published by TIGR.  Subsequent rounds of gene calling will produce
different identifiers that may or may not be easily mapped back to
either of these names.  We recommend that authors choosing to publish
information about specific gene models take care to identify the exact
sequence used in their studies.  Two possible ways to do this are to:

1) Identify the coordinates of the sequence used in your study relative
to the genomic sequence submitted by TIGR to the Whole Genome Shotgun
sequence record at NCBI.  These records can be found at:
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=59717367
Find the proper coordinates with the TGD BLAST server
(http://seq.ciliate.org/cgi-bin/blast-tgd.pl) by searching the "T.
thermophila Macronuclear Genome (TIGR v2)" dataset with the sequence of
the preliminary gene model.  The coordinates of the aligned  sections
can be identified, and a link to the GenBank entry is provided.

2) Make the sequence used in your study available as "Supplementary
Materials".

Before publishing any studies using the Tetrahymena genome sequence,
please review TIGR's data release policy at:
http://www.tigr.org/tdb/e2k1/ttg/release.shtml

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

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