Comparing protein sequences.

Scott Coutts SPAMFILTER-scott.coutts at med.monash.edu.au
Wed Dec 1 17:48:03 EST 2004


Stefek Borkowski wrote:

> Hi,
> 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,
> Stefek

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.

Good luck!

Scott.



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