Zebrafish Gene Index

John Quackenbush johnq at tigr.org
Fri Mar 19 10:48:53 EST 1999


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The Institute for Genomic Research (TIGR) would like to announce the
release of the Zebrafish Gene Index (ZGI), Version 2.0.

The Zebrafish Gene Index represents an attempt to identify the unique
transcripts represented by the publicly available EST sequence data
deposited into GenBank. EST sequences are downloaded from GenBank,
cleaned to remove any remaining vector, linker, and low-quality
sequence, and screened to remove mitochondrial and ribosomal sequences.
The remaining ESTs are then compared pair-wise to each other to identify
overlapping sequences and produce clusters. The EST sequences within
each cluster are then assembled at high stringency, producing Tentative
Consensus (TC) sequences that are, in general, longer and more reliable
than the individual constituent EST sequences. ZGI 2.0 includes 10,317
EST sequences, 4,757 which have been assembled into 1,221 consensus
sequences. The remaining 5,560 ESTs either did not cluster or were
separated out during the assembly process and these are identified as
singletons in our current release.

All data in ZGI are freely available to researchers at nonprofit
institutions using it for non-commercial purposes.  The index can be
accessed at <http://www.tigr.org/tdb/zgi/zgi.html>.

Commercial organizations can request a license to ZGI by sending e-mail
to <license at tigr.org>.

As EST data are made available in dbEST from the WashU-MPIMG zebrafish
Expressed Sequence Tag project, we will regularly update the ZGI to
reflect our best estimate of the transcripts that underlie the
Zebrafish EST sequences.

Also please note that we will soon add a BLAST-search utility so that
users of the ZGI can more easily search the database. We plan to have
this new utility available sometime next week.

John Quackenbush
The Institute for Genomic Research
9712 Medical Center Drive
Rockville, MD 20850
301-838-3528 (voice)
301-838-0208 (fax)
<http://www.tigr.org/~johnq>

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