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unfinished Arabidopsis seq data?

Mike Cherry cherry at genome.stanford.edu
Wed Mar 29 12:10:29 EST 2000

Arabidopsis sequencing groups submit unfinished data to the High
Throughput Genomics (HTG) section of GenBank.  If you update GenBank
at your site you have these sequences.  If you don't update GenBank
you should be spending your time on that problem.  From the beginning
the AtDB BLAST and FASTA servers contained these unfinished sequences.
These resources are now available from the new Arabidopsis community
database at TAIR (www.arabidopsis.org).

For Arabidopsis sequencing the "time-gap" between first submission of
phase I sequence and release of annotated sequence has typically been
on the order of 1-2 months.

Depending on how agressive you want to be working with these HTG
sequences can be good or bad.  Since they are preliminary they do
change and require some analyses to be redone.  It all depends on your
need and ability to deal with change.


P.S. The CSHL-WASHU consortium puts unfinished sequences on their ftp
site weekly (I believe).  These sequences are also available from the
TAIR BLAST.  You can download them from ftp.cshl.org:/pub/sequences/

J. Michael Cherry, Ph.D.         Internet: cherry at genome.stanford.edu
Department of Genetics           Stanford University School of Medicine
Medical Center, Room M341        Stanford, California  94305-5120
Voice:    650-723-7541           FAX: 650-723-7016

>  Dear All:
>  I am not familiar with plant genomics. Recently, I heard from a chat that
>  there is usually a delay (is this true?) for the Arabidopsis sequence data
>  to be submitted to GenBank. Obviously, you can get a competitive advantage
>  to exploit this 'time-gap'. Some faculty asked us to collect all these
>  unfinished data daily. This way, the researcher can get three to six months
>  ahead of others.
>  Where are the unfinished Arabidopsis sequence data? How often are they
>  released (hourly? daily? monthly?)???? Does it make sense to collect and
>  compile these data from the TIGR, WashU, and several other sites daily?
>  We are brain-storming for this project, but have not started yet. Pros or
>  cons? Anybody know a group had already done this?
>  Simon
>  =============================================================
>           Simon Lin, M.D.
>           Duke Bioinformatics Shared Resource
>           http://www.canctr.mc.duke.edu/bioinformatics
>  Mailing address:
>           Hanes 248, Trent Drive
>           Box 3958, Duke University Medical Center
>           Durham, NC 27710
>           Ph: (919) 681-9646
>           FAX: (919) 681-8028
>           lin00025 at mc.duke.edu
>  =============================================================
>  Street address for express mail only: Jones Bldg., Room 133, Research Drive,
>  Duke University Medical Center, Durham, NC 27708
>  ---


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