[Bioperl-l] How to run Blast with a user defined DNA substitution scoring matrix?

[Torsten Seemann]

> I need to run blast using a user defined DNA scoring matrix (may sound funny but I am really serious). Can anybody give me a hint on it?

This mailing list is for help with using BioPerl modules, not for
general bioinformatics tools.

In Bio::Tools::Run::StandAloneBlast->new(), you can pass in any valid
parameter for 'blastall'
and it will be used when running blastall.

Standard blastall has parameters  for match (-q) and mismatch (-r),
but I don't believe it can do a full custom matrix for DNA alignments.

You should look the the EMBOSS tools "water" and "needle" which take a
"-datafile" parameter to supply a custom DNA matrix.

--Torsten