Yep, I used BLAST, followed my mview (http://mathbio.nimr.mrc.ac.uk/~nbrown/mview/) to prepare an alignment from the BLAST-report.
in reply to Re: Similarity of strings
in thread Similarity of strings
But MVIEW doesn't provide the similarity stuff (but does provide e-value, score, and some other things) and I don't have the guts to parse the complete BLAST-report (which can be very big sometimes) just to get the similarity.
I prefer to check only those sequences which are of interest to me directly.