ESTs now displayed in TAIR SeqViewer

Eva Huala huala at acoma.Stanford.EDU
Tue May 21 14:28:35 EST 2002


Dear Arabidopsis researchers,

We have upgraded the TAIR SeqViewer map tool to display ESTs in
the new Transcripts band.  To view the new data, go to

   http://arabidopsis.org/servlets/sv

and click on a green chromosome to open a closeup view.  To see
the EST matches in more detail, zoom in to 40 kb or less using
the control at the left, and change "3 rows" to "all (or 6) rows"
(middle left control panel) to see all the ESTs.  Click on the
EST to view a detail page containing information including
sequence links.

We have also added mouseover information to genes, clones and ESTs
to increase the amount of information visible in the closeup view.
Each popup mouseover box contains a link to a 10 kb nucleotide
sequence window displaying the object in the context of the
chromosome sequence.  A nucleotide view can also be opened at any
point along the chromosome by clicking on the gray sequence ruler.

The ESTs were placed on the genome map using a combination of BLAST
and SIM4 to match each EST directly to the chromosome sequence.
Matching EST segments from a single EST are shown as thick gray bars
connected by a thin gray line.

Within a few weeks we will add full length mRNAs to the transcript
band, to allow users to easily distinguish which gene models are
supported by transcripts.

Please send comments/suggestions to curator at arabidopsis.org

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Eva Huala                         	huala at acoma.stanford.edu
The Arabidopsis Information Resource	FAX: (650) 325-6857
Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 310
Department of Plant Biology		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
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