Arabidopsis chromosome 2 data

Xiaoying Lin xlin at tigr.org
Sun Jan 9 00:56:48 EST 2000


Dear all,

This posting is to announce the availability of the data of chromosome 2
sequence and analysis recently published by the TIGR group (Lin & Kaul et
al. 1999, Nature, 402:761-768).


At TIGR WEBSITE:

While the data on each individual clone is still available at
http://www.tigr.org/at/agad , for the sequence and annotation of the
entire chromosome, please go to http://www.tigr.org/tdb/ath1/htmls/ath1.html


At this site, users can download the files of: genomic DNA sequence,
transcript, coding sequence (CDS), 5' and 3' Untranslated Regions (UTRs),
as well the protein sequence.  A blast page has also been setup for users
to search the protein or transcript by sequence similarity.

The list of chromosome 2 genes can be browsed by functional categories and
searched either by key words (in gene names) or gene identifier
(At2gxxxxx).

Clone contigs on chromosome 2 are presented in a tabular and a graphical
format.  In the graphical contig page, besides the fully sequenced clones,
additional BACs were mapped to chromosome 2 by BAC end sequence match to
give additional choices of clones to get hold of the gene(s) of one's
interest.

There is a new link on this page that allow one to retrieve sequence and
annotation within a user-defined bp range on the chromosome

The data is from a new database still under construction at TIGR,
currently containing just the finished chromosome 2 data. The contents and
format of this page will change and things may not always work as expected
(we ask for your understanding :-).


At GenBank:

The accession for the whole chromosome is AE002093, this record has been
split into 255 sections by GenBank. Some users have 'noticed' that clone
information is missing at GenBank, and GenBank is adding such information
back to the records.  One can also view chromosome data through the new
GenBank Genome page:
http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?gi=146&db=Genome


I would like to thank my colleagues at the TIGR informatics department for
helping with the new web page and GenBank for processing the record in a
timely manner. Please address questions/comments to at at tigr.org.


Regards,

Xiaoying Lin
Assistant Investigator
The Institute for Genomic Research
9712 Medical Center Drive, Rockville, MD 20850
301-838-3530    Fax: 301-838-0208    E-mail: xlin at tigr.org

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