[Arabidopsis] Searching the Whole Arabidopsis Genome for a Motif

[Norman Warthmann]

Dear Siobhan,

I recommend you use the new BLAST (beta) version on the NCBI blast website

http://www.ncbi.nlm.nih.gov/BLAST/beta

There you can do a "BLAST Assembled Genomes" against the "Arabidopsis 
thaliana"; since your sequences are short, make sure you switch the 
filter off and reduce the word size to 8.

database: genome (default)
program: megaBLAST (default)
filter: none
Advanced options: -W 8

cheers

Norman

Norman Warthmann
Max-Planck-Institute for Developmental Biology
Dept. Molecular Biology