Comparing protein sequences.
SPAMFILTER-scott.coutts at med.monash.edu.au
Wed Dec 1 17:48:03 EST 2004
Stefek Borkowski wrote:
> I have a problem. I would compare 2 known sequences of ca. 130 amino
> acid residues, namely human epidermal fatty acid-binding protein vs.
> human ileal fatty acid-binding protein. I have tried WWW BLAST at
> http://www.ncbi.nlm.nih.gov/blast/ - chosing "Protein-protein BLAST
> (blastp)", but unfortunately cannot find my match in the report of the
> program. I suspect that the homology may be too little so BLAST skips
> this pair of proteins in the report. How do I do it then? Maybe I should
> change something in the settings of BLAST interface? Is there a kind of
> software (maybe working offline) which accepts two sequences as input
> and simply compares the two of them?
> Thank you for any help you can offer.
> Kind regards from Poland,
You'd be better off finding both sequences (you can do this by simply
using a keyword search) and then doing an alignment of the two
sequences. You can do this on the web, using one of the 'clustal'
programs, or you can download a stand-alone version of clustal and view
your alignment using another downloadable program called 'genedoc'. I
dont have the web addresses on hand at the moment, but you can easily
find them with a google search.
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