And a shallow scoring matrix: MD10 or MD20.
Of course it's not an actual motif search, you can only feed it a single
query. How "good" is your motif? Is there enough data to build an HMM?
If so, you could use GeneWise to search a nucleotide database with your
hmm.
-Aaron
On 24 Mar 2000, Dr. Greg Quinn wrote:
> TFASTX with a word size of 1?
>> Jeffrey Keen (t.j.keen at leeds.ac.uk) wrote:
> : Can anyone suggest how I can search a nucleotide database with a short
> : protein motif. I had a look at EMBOSS but didn't see anything that might
> : do the job.
> :
> : Thanks
> :
> : Jeffrey Keen
>>
--
o ~ ~ ~ ~ ~ ~ o
/ Aaron J Mackey \
\ Dr. Pearson Laboratory /
\ University of Virginia \
/ (804) 924-2821 \
\ amackey at virginia.edu /
o ~ ~ ~ ~ ~ ~ o
