[Bioperl-l] conservative amino acid change?

[Heikki Lehvaslaiho]

Hilmar Lapp wrote:
> 
> Heikki Lehvaslaiho wrote:
> >
> > My implementation has the BLOSUM62 matrix inside the package. I can
> > not remember matrixes never being discussed in bioperl context. Other
> > bio* projects might have a selection of standard similarity matrixes
> > included. (?) Should we have them? And classes dealing with them?
> >
> 
> I think we should. It is definitely going to be useful for other
> modules, too.


OK. I'll write the modules:

Bio::Matrix::SimilarityMatrixI
	id()
	name()
	moltype()
	pam()
	max()
	min()
	def()
	deletion()
	similarity_score()
	
Bio::Matrix::SimilarityMatrix
Bio::Matrix::SimilarityMatrixIO
Bio::Matrix::SimilarityMatrixIO::full
Bio::Matrix::SimilarityMatrixIO::half

or something like that...


We'll need a data directory to place the default matrixes in. What
would be the best (platform independent) way of refering to files
within bioperl?

	-Heikki