wheat ESTs

[Lenny Teytelman]

Dear Mike,

If the EST is from dbEST, you can find whether it has been positioned on
the rice genome by searching for the accession at:
	http://www.gramene.org/perl/SeqTable
Just enter the accession into the 'Lookup' field, and if the EST was
mapped, you will get back the clones and positions of the alignments.  You
may then follow the link to view the region in the Genome Browser.

If the EST is not part of dbEST, you can do a blast search using its
sequence against the rice genome or the dbEST library.  Just select 'Rice
IRGSP Clones' or 'Triticum Aestivum ESTs' in the 'Database' drop-down
menu at:
http://www.gramene.org/gramene/searches/blast
 
Another option is to simply download the list of the ESTs and the clones
to which they align from:
ftp://brie.cshl.org/pub/gramene/insilico_data/ESTs/

The 'final_triticum_est_bacs_052202.dat.gz' file contains all of the
results for the wheat EST alignments.  The fields in the file are:
        Internal_ID
	EST_Accession
        EST_Start
        EST_Stop
        Clone_ACC
        Clone_Version
        Clone_Start
        Clone_Stop
        Percent_Identity_of_match

Regards,

Lenny

PS  The 72,000 is the total number of alignments, but some ESTs can hit
two or three times.  The actual number of distinct wheat ESTs is 49,146.
Please see
http://www.gramene.org/documentation/EST/triticum_est_rice_genome.txt
for more information on the wheat alignments.


> Dear Lenny: 
> I’m an entomologist at Kansas State University leading a group of students & 
> post docs to map genes for aphid resistance in wheat.
> 
> I read in Grain Genes recently where you have identified homologies of 72,000 
> wheat ESTs to rice BAC/PACs from a set of 167,000 ESTs examined 20 June '02.
> 
> I have no bioinformatics training, but have acquired several wheat chromosome 
> 7DS ESTs from the USDA Lab in Albany, CA.  Although none are closely linked to 
> our genes of interest, we know where they fit into an overall emerging linkage 
> map, primarily on wheat chromosome 7.
> 
> My questions for you are: how do I locate a given EST in your list, and once I 
> find one, how do I match it with a given rice BAC/PCS?    Mike Smith
> 
> 
> 

-- 
Lenny Teytelman
Cold Spring Harbor Laboratory
516-367-8864
teytelman at cshl.org