Comparing protein sequences.

Stefek Borkowski stefek at killspam.edu
Wed Dec 1 14:41:35 EST 2004

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,

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