One of the challenges in building gene indices is the increasing quantity
of data from Genomic Sequencing Projects. In an effort to integrate those
annotated genomic data, we have incorporated the predicted transcripts
into building TIGR Gene index. In this new build, 1,113 Predicted
Transcripts that were annotated based on EST hits, 36,622 cleaned EST and
2,002 ET (Expressed Transcript) sequences were used and assembled into
5,811 Tentative Consensus (TC) sequences with 10,138 singletons left. Due
to the incorporation of Predicted Transcripts and use of cleaned ESTs, the
unique set of transcripts was dramatically decreased from 24,977 down to
15,949, a 34 % of reduction.
More importantly, the stringent assembly in building Arabidopsis gene
index helps mapping of individual ESTs onto Arabidopsis Chromosomes, which
allows users of the genomic sequence to identify 'physical clones' encoding
genes of potential interest and users of the AtGI to consider transcripts
in a genomic context. The new AtGI is available at
>What makes this new build of AtGI notable, however, can be seen by opening
>the AtGI page at >http://www.tigr.org/tdb/agi/searching/reports.html and
>looking, for >example, at TC# 56493.
>>If you look at the assembly for this TC, you will note that sequence #1
>>>is a sequence from AGAD - the Arabidopsis Genomic Annotation database.
>>It is a >predicted transcript from the Arabidopsis sequencing project.
The TIGR Gene Indices are available via a free license for academic and
nonprofit use; commercial licenses are available for a fee. Parties
interested in obtaining a license should visit
<http://www.tigr.org/tdb/license.html> or write to license at tigr.org.
Feng Liang, PhD
The Institute for Genomic Research
The Institute for Genomic Research (TIGR) has released a new build of
Arabidopsis Gene Index.