[Bioperl-l] Substitution matrix format for Bio::Tools::pSW (Wise2)

[Benjamin Berman]

Sorry if this has come up before, I couldn't find any reference to it.

Why is the subsitution matrix format for Bio::Tools::pSW (actually from 
Wise2) different from that used by blast?  From what I can tell, the normal 
blast format includes the alphabet characters as the first element of every 
row and every column, while the Wise2 format includes them only as the 
first element of every column.

I guess it's not a practical problem because the conversion seems pretty 
trivial.  But I'm curious to know if I've got this straight or if I'm 
missing something.

It would probably be nice to include some explanation of this in the 
documentation for pSW - to keep newbies like me from getting tripped up.

Thanks,
ben.


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Benjamin Berman
Rubin Lab, 539 Life Sciences Addition
Department of Molecular and Cell Biology
University of California, Berkeley
benb@fruitfly.org