The database on the genes that Arabidopsis researchers have

Keith Bradnam krb at sanger.ac.uk
Mon Aug 20 04:03:10 EST 2001


On 17 Aug 2001, Motoaki Seki wrote:

>  Dear Sir,
>
>  I would like to know the database on the genes that  Arabidopsis researchers
>  have cloned and sequenced (not EST or genome sequencing project).  I would
>  really appreciate it if somebody could offer me the information on the
>  database.
>  Any information or suggestions would be much appreciated.

Hi Motoaki,

You may be able to get the information you need from the Arabidopsis
Genome Resource (AGR) database (http://ukcrop.net/agr).  This contains all
sequences that are in EMBL, but if you go to the AGR query page:

http://ukcrop.net/perl/ace/query/AGR

and then paste in the following query:

Find Sequence; !AGI_sequence; !Arabidopsis_EST; !Arabidopsis_GSS; 
!Insert_sequence

This will return a list of about 60,000 sequences which have not been
annotated as an AGI clone sequence, EST, Genome survey sequence (GSS) or
insert sequence.  If you just want to find predicted genes add ';*cds' to
the above query (omit the apostrophes).

This will return you a list of about 40,000 predicted genes.  These have
all been blast searched against plant protein sequences in SwissProt and
all Arabidopsis genomic DNA.

Hope this helps,

Keith

~  Keith Bradnam - WormBase group: http://wormbase.sanger.ac.uk/
~
~  The Sanger Centre, Wellcome Trust Genome Campus
~  Hinxton, Cambridge, CB10 1SA, UK.  Tel (01223) 497516




More information about the Arab-gen mailing list