[BioRuby] custom blast scoring matrix

[Robert Citek]

Hello all,

I would like to create a custom BLAST scoring matrix that I can use
with NCBI's blastall.  For example, let's say I want to create a
modified BLOSUM62 matrix called BLOSUM62ar, where the A:R score is now
2 instead of -1.

Some questions that I have:

1) is this possible?
2) if it is, where can I find documentation which describes how to do this?
3) is the blast output different from a regular blast?
4) if it is different, does bio-ruby have blast parsers that can parse
the output?

Thanks in advance for any pointers and suggestions.

Regards,
- Robert