




Description 
Common substitution matrices for alignments.
When in doubt, use BLOSUM62.
Consult http://www.ncbi.nlm.nih.gov/blast/blast_whatsnew.shtml#20051206
for some hints on good parameters for nucleotide alignments.
See also http://en.wikipedia.org/wiki/Substitution_matrix for a
summary about the difference between the different matrices.


Synopsis 




BLOSUM matrices


For BLOSUM matrices, the associated number determines the
similarity of the sequences the matrices are derived from.
Henikoff, S. and Henikoff, J. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA. 89(biochemistry): 10915  10919 (1992).



BLOSUM45 matrix, suitable for distantly related sequences



The standard BLOSUM62 matrix.



BLOSUM80 matrix, suitable for closely related sequences.


PAM matrices


For PAM matrics, the number indicates the number of mutations
that have occurred between the sequences that are compared.
Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C. A model of evolutionary change in proteins. In "Atlas of Protein Sequence and Structure" 5(3) M.O. Dayhoff (ed.), 345  352 (1978).



The standard PAM30 matrix



The standard PAM70 matrix.


BLASTn defaults, for nucleotide sequences



Blast defaults, use with gap_open = 5 gap_extend = 3
This should really check for valid nucleotides, and perhaps be more
lenient in the case of Ns. Oh well.


Generic and simple matrix generator



Construct a simple matrix from match score/mismatch penalty


Produced by Haddock version 2.6.1 