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blosum.go
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package seq
// SubstMatrix corresponds to a substitution matrix and an alphabet that is
// used in sequence alignment algorithms. The matrix given should be square,
// with rows and columns equivalent to the length of the alphabet. (This means
// that if your substitution matrix includes gap penalties, then the alphabet
// should also have a gap character.)
type SubstMatrix struct {
Alphabet Alphabet
Scores [][]int
}
var (
identity = [][]int{
{
2, -1, -1, -1, 0, 0,
},
{
-1, 2, -1, -1, 0, 0,
},
{
-1, -1, 2, -1, 0, 0,
},
{
-1, -1, -1, 2, 0, 0,
},
{
0, 0, 0, 0, 0, 0,
},
{
0, 0, 0, 0, 0, 0,
},
}
// A standard BLOSUM62 substitution matrix for amino acid sequences.
SubstBlosum62 = SubstMatrix{AlphaBlosum62, blosum62}
// An identity substitution matrix for DNA sequences.
SubstDNA = SubstMatrix{AlphaDNA, identity}
// An identity substitution matrix for DNA sequences.
SubstRNA = SubstMatrix{AlphaRNA, identity}
)
// The indices correspond to alpha62, and can be retrieved using the
// alpha62map. The last element in each column/row is the gap penalty.
var blosum62 = [][]int{
{
4.0, -2.0, 0.0, -2.0, -1.0, -2.0, 0.0, -2.0, -1.0, -1.0, -1.0, -1.0,
-2.0, -1.0, -1.0, -1.0, 1.0, 0.0, 0.0, -3.0, 0.0, -2.0, -1.0, -4.0,
},
{
-2.0, 4.0, -3.0, 4.0, 1.0, -3.0, -1.0, 0.0, -3.0, 0.0, -4.0, -3.0, 3.0,
-2.0, 0.0, -1.0, 0.0, -1.0, -3.0, -4.0, -1.0, -3.0, 1.0, -4.0,
},
{
0.0, -3.0, 9.0, -3.0, -4.0, -2.0, -3.0, -3.0, -1.0, -3.0, -1.0, -1.0,
-3.0, -3.0, -3.0, -3.0, -1.0, -1.0, -1.0, -2.0, -2.0, -2.0, -3.0, -4.0,
},
{
-2.0, 4.0, -3.0, 6.0, 2.0, -3.0, -1.0, -1.0, -3.0, -1.0, -4.0, -3.0,
1.0, -1.0, 0.0, -2.0, 0.0, -1.0, -3.0, -4.0, -1.0, -3.0, 1.0, -4.0,
},
{
-1.0, 1.0, -4.0, 2.0, 5.0, -3.0, -2.0, 0.0, -3.0, 1.0, -3.0, -2.0, 0.0,
-1.0, 2.0, 0.0, 0.0, -1.0, -2.0, -3.0, -1.0, -2.0, 4.0, -4.0,
},
{
-2.0, -3.0, -2.0, -3.0, -3.0, 6.0, -3.0, -1.0, 0.0, -3.0, 0.0, 0.0,
-3.0, -4.0, -3.0, -3.0, -2.0, -2.0, -1.0, 1.0, -1.0, 3.0, -3.0, -4.0,
},
{
0.0, -1.0, -3.0, -1.0, -2.0, -3.0, 6.0, -2.0, -4.0, -2.0, -4.0, -3.0,
0.0, -2.0, -2.0, -2.0, 0.0, -2.0, -3.0, -2.0, -1.0, -3.0, -2.0, -4.0,
},
{
-2.0, 0.0, -3.0, -1.0, 0.0, -1.0, -2.0, 8.0, -3.0, -1.0, -3.0, -2.0,
1.0, -2.0, 0.0, 0.0, -1.0, -2.0, -3.0, -2.0, -1.0, 2.0, 0.0, -4.0,
},
{
-1.0, -3.0, -1.0, -3.0, -3.0, 0.0, -4.0, -3.0, 4.0, -3.0, 2.0, 1.0,
-3.0, -3.0, -3.0, -3.0, -2.0, -1.0, 3.0, -3.0, -1.0, -1.0, -3.0, -4.0,
},
{
-1.0, 0.0, -3.0, -1.0, 1.0, -3.0, -2.0, -1.0, -3.0, 5.0, -2.0, -1.0,
0.0, -1.0, 1.0, 2.0, 0.0, -1.0, -2.0, -3.0, -1.0, -2.0, 1.0, -4.0,
},
{
-1.0, -4.0, -1.0, -4.0, -3.0, 0.0, -4.0, -3.0, 2.0, -2.0, 4.0, 2.0,
-3.0, -3.0, -2.0, -2.0, -2.0, -1.0, 1.0, -2.0, -1.0, -1.0, -3.0, -4.0,
},
{
-1.0, -3.0, -1.0, -3.0, -2.0, 0.0, -3.0, -2.0, 1.0, -1.0, 2.0, 5.0,
-2.0, -2.0, 0.0, -1.0, -1.0, -1.0, 1.0, -1.0, -1.0, -1.0, -1.0, -4.0,
},
{
-2.0, 3.0, -3.0, 1.0, 0.0, -3.0, 0.0, 1.0, -3.0, 0.0, -3.0, -2.0, 6.0,
-2.0, 0.0, 0.0, 1.0, 0.0, -3.0, -4.0, -1.0, -2.0, 0.0, -4.0,
},
{
-1.0, -2.0, -3.0, -1.0, -1.0, -4.0, -2.0, -2.0, -3.0, -1.0, -3.0, -2.0,
-2.0, 7.0, -1.0, -2.0, -1.0, -1.0, -2.0, -4.0, -2.0, -3.0, -1.0, -4.0,
},
{
-1.0, 0.0, -3.0, 0.0, 2.0, -3.0, -2.0, 0.0, -3.0, 1.0, -2.0, 0.0, 0.0,
-1.0, 5.0, 1.0, 0.0, -1.0, -2.0, -2.0, -1.0, -1.0, 3.0, -4.0,
},
{
-1.0, -1.0, -3.0, -2.0, 0.0, -3.0, -2.0, 0.0, -3.0, 2.0, -2.0, -1.0,
0.0, -2.0, 1.0, 5.0, -1.0, -1.0, -3.0, -3.0, -1.0, -2.0, 0.0, -4.0,
},
{
1.0, 0.0, -1.0, 0.0, 0.0, -2.0, 0.0, -1.0, -2.0, 0.0, -2.0, -1.0, 1.0,
-1.0, 0.0, -1.0, 4.0, 1.0, -2.0, -3.0, 0.0, -2.0, 0.0, -4.0,
},
{
0.0, -1.0, -1.0, -1.0, -1.0, -2.0, -2.0, -2.0, -1.0, -1.0, -1.0, -1.0,
0.0, -1.0, -1.0, -1.0, 1.0, 5.0, 0.0, -2.0, 0.0, -2.0, -1.0, -4.0,
},
{
0.0, -3.0, -1.0, -3.0, -2.0, -1.0, -3.0, -3.0, 3.0, -2.0, 1.0, 1.0,
-3.0, -2.0, -2.0, -3.0, -2.0, 0.0, 4.0, -3.0, -1.0, -1.0, -2.0, -4.0,
},
{
-3.0, -4.0, -2.0, -4.0, -3.0, 1.0, -2.0, -2.0, -3.0, -3.0, -2.0, -1.0,
-4.0, -4.0, -2.0, -3.0, -3.0, -2.0, -3.0, 11.0, -2.0, 2.0, -3.0, -4.0,
},
{
0.0, -1.0, -2.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0,
-1.0, -2.0, -1.0, -1.0, 0.0, 0.0, -1.0, -2.0, -1.0, -1.0, -1.0, -4.0,
},
{
-2.0, -3.0, -2.0, -3.0, -2.0, 3.0, -3.0, 2.0, -1.0, -2.0, -1.0, -1.0,
-2.0, -3.0, -1.0, -2.0, -2.0, -2.0, -1.0, 2.0, -1.0, 7.0, -2.0, -4.0,
},
{
-1.0, 1.0, -3.0, 1.0, 4.0, -3.0, -2.0, 0.0, -3.0, 1.0, -3.0, -1.0, 0.0,
-1.0, 3.0, 0.0, 0.0, -1.0, -2.0, -3.0, -1.0, -2.0, 4.0, -4.0,
},
{
-4.0, -4.0, -4.0, -4.0, -4.0, -4.0, -4.0, -4.0, -4.0, -4.0, -4.0, -4.0,
-4.0, -4.0, -4.0, -4.0, -4.0, -4.0, -4.0, -4.0, -4.0, -4.0, -4.0, -4.0,
},
}