For an example that uses the blosum 62 matrix see the junit test org.biojava.bio.align.SubstitutionMatrixTest
Andreas On 17 Sep 2007, at 11:09, Richard Holland wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > @see org.biojava.bio.align.SubstitutionMatrix > > Basically it doesn't include any matrices, but the above class will > load > matrix definition files the user has downloaded from the NCBI FTP > site, > so you can obtain standard matrices that way. > > > Matthew Pocock wrote: >> Somebody asked me: >> >>> I was wondering whether BioJava provides standard scoring matrices >>> (e.g. BLOSUM62, etc.) as "constants" anywhere for doing >>> alignments. I >>> couldn't seem to find this anywhere in the code but, admittedly, >>> have >>> not looked very closely yet. >> >> And rather embarasingly, I don't know the answer. Does someone here? >> >> Matthew >> _______________________________________________ >> Biojava-l mailing list - [email protected] >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.2.2 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iD8DBQFG7lJ14C5LeMEKA/QRAhzZAJ0bcGko6nLMFXcRsvk092Iz2WBJJgCeJBm9 > 62Vv3F3jp6Mv2Zcoyx4yln0= > =bAYC > -----END PGP SIGNATURE----- > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l ----------------------------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK +44 (0) 1223 49 6891 ----------------------------------------------------------------------- -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
