motif search

Aaron J Mackey ajm6q at virginia.edu
Fri Mar 24 15:54:54 EST 2000


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
> 
> 

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