Yep, I used BLAST, followed my mview (http://mathbio.nimr.mrc.ac.uk/~nbrown/mview/) to prepare an alignment from the BLAST-report.
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.
Cheerz, Micha | [reply] |
Perhaps bioperl has a BLAST parser you could use? (I've never used their parsers, so I cannot comment further.)
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I'm using BioPerl already, but I think parsing a 40-200 Mb BLAST-report is over the top and won't save much time (if at all) over calculating the similarities by myself. In fact, that would be a real memory-filler. ;-)
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