 | bio-0.3.3.2: A bioinformatics library | Source code | Contents | Index |
| Bio.Alignment.Matrices |
| Contents |
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.
| blosum45 :: (Char, Char) -> Int |
| blosum62 :: (Char, Char) -> Int |
| blosum80 :: (Char, Char) -> Int |
| pam30 :: (Char, Char) -> Int |
| pam70 :: (Char, Char) -> Int |
| blastn_default :: Num a => (Chr, Chr) -> a |
| simpleMx :: Num a => a -> a -> (Chr, Chr) -> a |
| blosum45 :: (Char, Char) -> Int | Source |
| blosum62 :: (Char, Char) -> Int | Source |
| blosum80 :: (Char, Char) -> Int | Source |
| pam30 :: (Char, Char) -> Int | Source |
| pam70 :: (Char, Char) -> Int | Source |
| blastn_default :: Num a => (Chr, Chr) -> a | Source |
The standard BLOSUM62 matrix.
The standard BLOSUM80 matrix.
The standard PAM30 matrix
The standard PAM70 matrix.
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.
| simpleMx :: Num a => a -> a -> (Chr, Chr) -> a | Source |