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TAIR's New Polymorphism/Allele Search

Tanya Berardini tberardi at acoma.Stanford.EDU
Wed Oct 16 17:49:14 EST 2002

Dear Arabidopsis researchers,

We are pleased to announce the release of the Polymorphism/Allele Search
at TAIR.  Give it a test run at:


Polymorphisms at TAIR include both natural (ecotype) variants and induced
mutations.  Use this search to find visible polymorphisms (for example,
classical markers like ap1) and sequence polymorphisms (including
substitutions, insertions, and deletions).  You can also find
polymorphisms that produce an altered restriction digest pattern or PCR
product length.

Searchable data (around 115,500 total entries) includes over 9000 SNPs
submitted by the Stanford Genome Consortium, almost 600 characterized
polymorphisms from the Arabidopsis Tilling Project, and over 67000 T-DNA
insertions from the SALK Institute, as well as alleles from lines
submitted to the Arabidopsis Biological Resource Center (ABRC) and
individual submissions from research laboratories all over the world.

You can search by polymorphism/gene/allele/submitter name and refine your
search based on various polymorphism features and/or map location.
Search by the locus name (for example, At1g01230) of your favorite gene to
find any associated polymorphisms. The result page summarizes all of the
matching hits to your input query in one place. Clicking on individual
result lines links you to a Polymorphism detail page which contains
specific information like mutagen, gene models which are affected by the
polymorphism, sequence variation, map position and references, among
others. You can link to the SeqViewer to see the position of the
polymorphism in its genomic context or link to the Seed Stock search to
see if the ABRC has stocks pertaining to this polymorphism. The T-DNA
lines are not yet viewable on the SeqViewer but will be within the next
few weeks.

Help documentation gives an overview and introduction to using the search.


We thank the research community for your data contributions and look
forward to your feedback on these new pages.

All the best,

The TAIR Team
curator at arabidopsis.org

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


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