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| 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.
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| Synopsis |
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| BLOSUM matrices
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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).
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| BLOSUM45 matrix, suitable for distantly related sequences
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| The standard BLOSUM62 matrix.
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| BLOSUM80 matrix, suitable for closely related sequences.
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| PAM matrices
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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).
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| The standard PAM30 matrix
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| The standard PAM70 matrix.
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| BLASTn defaults, for nucleotide sequences
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| 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.
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| Generic and simple matrix generator
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| Construct a simple matrix from match score/mismatch penalty
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| Produced by Haddock version 2.6.1 |
