A couple of possibilities, the Smith Waterman Search at EBI works quite
well with short sequences, visit:
and just use the default settings, there's not much you can do with the
sensitivity of this search.
You can do a BLAST search but you need to have access to a BLAST version
that allows you play with the "sensitivity" setting. You need to alter the
"Expect" setting way out beyond what most informatics services generally
allow. You used to be able to do this at NCBI but, with the introduction of
their fancy pull down menus, you can only set "Expect" to 1000, to have it
work with short sequences, you need to set it higher and higher (I have
used 100,000) to get a result.
I have had a look around the web this morning and can't find a public
access version of BLAST that will allow you to do this anymore. Perhaps you
have access to an in-house version of BLAST (or FASTA can be used in the
same way) that can give you free access to the "Expect" setting? Our
national genomics service, ANGIS, has maintained the ability to do this,
unfortunately it is a subscription service so you would have to pay a small
fee for access to their services (in my opinion, money well spent). They
can be visited at: http://www.angis.org.au
You can always investigate running BLAST locally on a desktop, it will be
slow but you will have complete control.
Regards and good luck.....Ken
>Could someone PLEASE give me a simple way to do a search for a protein
>sequence using ~5 residues
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Ken I. Mitchelhill
The John Holt Protein Structure Laboratory
St. Vincent's Institute of Medical Research
41 Victoria Parade
Fitzroy 3065 Victoria
AUSTRALIA
Telephone: 61-3-9288 2480
Facsimile: 61-3-9416 2676
Email: k.mitchelhill@medicine.unimelb.edu.au
Laboratory: http://www.medstv.unimelb.edu.au/WWWDOCS/SVIMRdocs/JHPSL.html
ABRF: http://www.abrf.org
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