[BiO BB] Multiple Alignments

Peter oledzki biopolak at yahoo.co.uk
Mon Mar 18 15:50:42 EST 2002

I've conducted blast searches on a protein sequence 
and i'm wondering if anyone knows the criteria for
choosing certain protein sequences to get a reliable
multiple alignment.

After considering e-value does the size of the protein
matter in the multiple alignment...say for example i
have a query sequence of 200 aa's and get a match with
a protein of 800 aa's, should I edit out the unrelated
aa for an alignment or leave them in?Or doesn't it

Thanks for any help 

Peter Oledzki


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