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Bio.Alignment.Matrices

Contents

BLOSUM matrices
PAM matrices
BLASTn defaults, for nucleotide sequences
Generic and simple matrix generator

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

blosum45 :: (Chr, Chr) -> Int
blosum62 :: (Chr, Chr) -> Int
blosum80 :: (Chr, Chr) -> Int
pam30 :: (Chr, Chr) -> Int
pam70 :: (Chr, Chr) -> Int
blastn_default :: Num a => (Chr, Chr) -> a
simpleMx :: Num a => a -> a -> (Chr, Chr) -> a

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 :: (Chr, Chr) -> Int | Source

BLOSUM45 matrix, suitable for distantly related sequences

blosum62 :: (Chr, Chr) -> Int | Source

The standard BLOSUM62 matrix.

blosum80 :: (Chr, Chr) -> Int | Source

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).

pam30 :: (Chr, Chr) -> Int | Source

The standard PAM30 matrix

pam70 :: (Chr, Chr) -> Int | Source

The standard PAM70 matrix.
BLASTn defaults, for nucleotide sequences

blastn_default :: Num a => (Chr, Chr) -> a | Source

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

simpleMx :: Num a => a -> a -> (Chr, Chr) -> a | Source

Construct a simple matrix from match score/mismatch penalty
Produced by Haddock version 2.4.2