Package Bio :: Package SubsMat :: Module MatrixInfo
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Module MatrixInfo

source code

Substitution matrices for use in alignments, etc.

The information on this page was originally obtained from Dr. Gerhard Vogt's page http://www.embl-heidelberg.de/~vogt/matrices/mlist1.html (dead link), and was extracted using a script.

You can view an archive copy of this webpage from 1999 here; https://web.archive.org/web/19991014010917/http://www.embl-heidelberg.de/%7Evogt/matrices/mlist1.html

Variables [hide private]
  available_matrices = ['benner6', 'benner22', 'benner74', 'blos...
  benner6 = {('A', 'A'): 2.5, ('A', 'C'): -1.7, ('A', 'P'): 1.1,...
  benner22 = {('A', 'A'): 2.5, ('A', 'C'): -1.2, ('A', 'P'): 0.8...
  benner74 = {('A', 'A'): 2.4, ('A', 'C'): 0.3, ('A', 'P'): 0.4,...
  blosum100 = {('A', 'A'): 5, ('B', 'A'): -3, ('B', 'B'): 4, ('B...
  blosum30 = {('A', 'A'): 4, ('B', 'A'): 0, ('B', 'B'): 5, ('B',...
  blosum35 = {('A', 'A'): 5, ('B', 'A'): -1, ('B', 'B'): 5, ('B'...
  blosum40 = {('A', 'A'): 5, ('B', 'A'): -1, ('B', 'B'): 5, ('B'...
  blosum45 = {('A', 'A'): 5, ('B', 'A'): -1, ('B', 'B'): 4, ('B'...
  blosum50 = {('A', 'A'): 5, ('B', 'A'): -2, ('B', 'B'): 5, ('B'...
  blosum55 = {('A', 'A'): 5, ('B', 'A'): -2, ('B', 'B'): 5, ('B'...
  blosum60 = {('A', 'A'): 4, ('B', 'A'): -2, ('B', 'B'): 4, ('B'...
  blosum62 = {('A', 'A'): 4, ('B', 'A'): -2, ('B', 'B'): 4, ('B'...
  blosum65 = {('A', 'A'): 4, ('B', 'A'): -2, ('B', 'B'): 4, ('B'...
  blosum70 = {('A', 'A'): 4, ('B', 'A'): -2, ('B', 'B'): 4, ('B'...
  blosum75 = {('A', 'A'): 4, ('B', 'A'): -2, ('B', 'B'): 4, ('B'...
  blosum80 = {('A', 'A'): 5, ('B', 'A'): -2, ('B', 'B'): 4, ('B'...
  blosum85 = {('A', 'A'): 5, ('B', 'A'): -2, ('B', 'B'): 4, ('B'...
  blosum90 = {('A', 'A'): 5, ('B', 'A'): -2, ('B', 'B'): 4, ('B'...
  blosum95 = {('A', 'A'): 5, ('B', 'A'): -3, ('B', 'B'): 4, ('B'...
  feng = {('A', 'A'): 6, ('A', 'C'): 2, ('A', 'P'): 5, ('A', 'S'...
  fitch = {('A', 'A'): 3, ('C', 'A'): 1, ('C', 'C'): 3, ('E', 'A...
  genetic = {('A', 'A'): 4.0, ('A', 'C'): -1.9, ('A', 'P'): 0.8,...
  gonnet = {('A', 'A'): 2.4, ('A', 'C'): 0.5, ('A', 'P'): 0.3, (...
  grant = {('A', 'A'): 215, ('A', 'C'): 61, ('A', 'E'): 130, ('A...
  ident = {('A', 'A'): 6, ('A', 'C'): -1, ('A', 'P'): -1, ('A', ...
  johnson = {('A', 'A'): 6.0, ('C', 'A'): -3.4, ('C', 'C'): 16.1...
  levin = {('A', 'A'): 2, ('A', 'D'): 0, ('A', 'E'): 1, ('A', 'G...
  mclach = {('A', 'A'): 8, ('A', 'F'): 1, ('A', 'G'): 3, ('A', '...
  miyata = {('A', 'A'): 1.25, ('A', 'C'): -0.14, ('A', 'P'): 1.1...
  nwsgappep = {('A', 'A'): 1.5, ('B', 'A'): 0.2, ('B', 'B'): 1.1...
  pam120 = {('A', 'A'): 3, ('B', 'A'): 0, ('B', 'B'): 4, ('B', '...
  pam180 = {('A', 'A'): 3, ('B', 'A'): 0, ('B', 'B'): 4, ('B', '...
  pam250 = {('A', 'A'): 2, ('B', 'A'): 0, ('B', 'B'): 3, ('B', '...
  pam30 = {('A', 'A'): 6, ('B', 'A'): -3, ('B', 'B'): 6, ('B', '...
  pam300 = {('A', 'A'): 2, ('B', 'A'): 0, ('B', 'B'): 3, ('B', '...
  pam60 = {('A', 'A'): 5, ('B', 'A'): -2, ('B', 'B'): 5, ('B', '...
  pam90 = {('A', 'A'): 4, ('B', 'A'): -1, ('B', 'B'): 4, ('B', '...
  rao = {('A', 'A'): 16, ('C', 'A'): 11, ('C', 'C'): 16, ('D', '...
  risler = {('A', 'A'): 2.2, ('C', 'A'): -1.5, ('C', 'C'): 2.2, ...
  structure = {('A', 'A'): 4, ('A', 'C'): -2, ('A', 'P'): -1, ('...
  __package__ = None
hash(x)
Variables Details [hide private]

available_matrices

Value:
['benner6',
 'benner22',
 'benner74',
 'blosum100',
 'blosum30',
 'blosum35',
 'blosum40',
 'blosum45',
...

benner6

Value:
{('A', 'A'): 2.5,
 ('A', 'C'): -1.7,
 ('A', 'P'): 1.1,
 ('A', 'S'): 1.4,
 ('A', 'T'): 1.7,
 ('C', 'C'): 12.1,
 ('D', 'A'): -0.6,
 ('D', 'C'): -3.7,
...

benner22

Value:
{('A', 'A'): 2.5,
 ('A', 'C'): -1.2,
 ('A', 'P'): 0.8,
 ('A', 'S'): 1.3,
 ('A', 'T'): 1.4,
 ('C', 'C'): 12.6,
 ('D', 'A'): -0.2,
 ('D', 'C'): -3.7,
...

benner74

Value:
{('A', 'A'): 2.4,
 ('A', 'C'): 0.3,
 ('A', 'P'): 0.4,
 ('A', 'S'): 1.1,
 ('A', 'T'): 0.7,
 ('C', 'C'): 11.8,
 ('D', 'A'): -0.3,
 ('D', 'C'): -3.2,
...

blosum100

Value:
{('A', 'A'): 5,
 ('B', 'A'): -3,
 ('B', 'B'): 4,
 ('B', 'C'): -5,
 ('B', 'D'): 4,
 ('B', 'E'): 0,
 ('B', 'F'): -5,
 ('B', 'G'): -2,
...

blosum30

Value:
{('A', 'A'): 4,
 ('B', 'A'): 0,
 ('B', 'B'): 5,
 ('B', 'C'): -2,
 ('B', 'D'): 5,
 ('B', 'E'): 0,
 ('B', 'F'): -3,
 ('B', 'G'): 0,
...

blosum35

Value:
{('A', 'A'): 5,
 ('B', 'A'): -1,
 ('B', 'B'): 5,
 ('B', 'C'): -2,
 ('B', 'D'): 5,
 ('B', 'E'): 0,
 ('B', 'F'): -2,
 ('B', 'G'): 0,
...

blosum40

Value:
{('A', 'A'): 5,
 ('B', 'A'): -1,
 ('B', 'B'): 5,
 ('B', 'C'): -2,
 ('B', 'D'): 6,
 ('B', 'E'): 1,
 ('B', 'F'): -3,
 ('B', 'G'): -1,
...

blosum45

Value:
{('A', 'A'): 5,
 ('B', 'A'): -1,
 ('B', 'B'): 4,
 ('B', 'C'): -2,
 ('B', 'D'): 5,
 ('B', 'E'): 1,
 ('B', 'F'): -3,
 ('B', 'G'): -1,
...

blosum50

Value:
{('A', 'A'): 5,
 ('B', 'A'): -2,
 ('B', 'B'): 5,
 ('B', 'C'): -3,
 ('B', 'D'): 5,
 ('B', 'E'): 1,
 ('B', 'F'): -4,
 ('B', 'G'): -1,
...

blosum55

Value:
{('A', 'A'): 5,
 ('B', 'A'): -2,
 ('B', 'B'): 5,
 ('B', 'C'): -3,
 ('B', 'D'): 5,
 ('B', 'E'): 1,
 ('B', 'F'): -4,
 ('B', 'G'): -1,
...

blosum60

Value:
{('A', 'A'): 4,
 ('B', 'A'): -2,
 ('B', 'B'): 4,
 ('B', 'C'): -3,
 ('B', 'D'): 4,
 ('B', 'E'): 1,
 ('B', 'F'): -3,
 ('B', 'G'): -1,
...

blosum62

Value:
{('A', 'A'): 4,
 ('B', 'A'): -2,
 ('B', 'B'): 4,
 ('B', 'C'): -3,
 ('B', 'D'): 4,
 ('B', 'E'): 1,
 ('B', 'F'): -3,
 ('B', 'G'): -1,
...

blosum65

Value:
{('A', 'A'): 4,
 ('B', 'A'): -2,
 ('B', 'B'): 4,
 ('B', 'C'): -3,
 ('B', 'D'): 4,
 ('B', 'E'): 1,
 ('B', 'F'): -3,
 ('B', 'G'): -1,
...

blosum70

Value:
{('A', 'A'): 4,
 ('B', 'A'): -2,
 ('B', 'B'): 4,
 ('B', 'C'): -4,
 ('B', 'D'): 4,
 ('B', 'E'): 1,
 ('B', 'F'): -4,
 ('B', 'G'): -1,
...

blosum75

Value:
{('A', 'A'): 4,
 ('B', 'A'): -2,
 ('B', 'B'): 4,
 ('B', 'C'): -4,
 ('B', 'D'): 4,
 ('B', 'E'): 1,
 ('B', 'F'): -4,
 ('B', 'G'): -1,
...

blosum80

Value:
{('A', 'A'): 5,
 ('B', 'A'): -2,
 ('B', 'B'): 4,
 ('B', 'C'): -4,
 ('B', 'D'): 4,
 ('B', 'E'): 1,
 ('B', 'F'): -4,
 ('B', 'G'): -1,
...

blosum85

Value:
{('A', 'A'): 5,
 ('B', 'A'): -2,
 ('B', 'B'): 4,
 ('B', 'C'): -4,
 ('B', 'D'): 4,
 ('B', 'E'): 0,
 ('B', 'F'): -4,
 ('B', 'G'): -1,
...

blosum90

Value:
{('A', 'A'): 5,
 ('B', 'A'): -2,
 ('B', 'B'): 4,
 ('B', 'C'): -4,
 ('B', 'D'): 4,
 ('B', 'E'): 0,
 ('B', 'F'): -4,
 ('B', 'G'): -2,
...

blosum95

Value:
{('A', 'A'): 5,
 ('B', 'A'): -3,
 ('B', 'B'): 4,
 ('B', 'C'): -4,
 ('B', 'D'): 4,
 ('B', 'E'): 0,
 ('B', 'F'): -5,
 ('B', 'G'): -2,
...

feng

Value:
{('A', 'A'): 6,
 ('A', 'C'): 2,
 ('A', 'P'): 5,
 ('A', 'S'): 5,
 ('A', 'T'): 5,
 ('C', 'C'): 6,
 ('D', 'A'): 4,
 ('D', 'C'): 1,
...

fitch

Value:
{('A', 'A'): 3,
 ('C', 'A'): 1,
 ('C', 'C'): 3,
 ('E', 'A'): 1,
 ('E', 'C'): 1,
 ('E', 'E'): 3,
 ('F', 'A'): 1,
 ('F', 'C'): 2,
...

genetic

Value:
{('A', 'A'): 4.0,
 ('A', 'C'): -1.9,
 ('A', 'P'): 0.8,
 ('A', 'S'): 0.1,
 ('A', 'T'): 0.9,
 ('C', 'C'): 5.5,
 ('D', 'A'): 1.0,
 ('D', 'C'): -1.6,
...

gonnet

Value:
{('A', 'A'): 2.4,
 ('A', 'C'): 0.5,
 ('A', 'P'): 0.3,
 ('A', 'S'): 1.1,
 ('A', 'T'): 0.6,
 ('C', 'C'): 11.5,
 ('D', 'A'): -0.3,
 ('D', 'C'): -3.2,
...

grant

Value:
{('A', 'A'): 215,
 ('A', 'C'): 61,
 ('A', 'E'): 130,
 ('A', 'F'): 38,
 ('A', 'H'): 134,
 ('A', 'I'): 114,
 ('A', 'L'): 89,
 ('A', 'N'): 192,
...

ident

Value:
{('A', 'A'): 6,
 ('A', 'C'): -1,
 ('A', 'P'): -1,
 ('A', 'S'): -1,
 ('A', 'T'): -1,
 ('C', 'C'): 6,
 ('D', 'A'): -1,
 ('D', 'C'): -1,
...

johnson

Value:
{('A', 'A'): 6.0,
 ('C', 'A'): -3.4,
 ('C', 'C'): 16.1,
 ('D', 'A'): -1.6,
 ('D', 'C'): -9.7,
 ('D', 'D'): 8.5,
 ('E', 'A'): -0.7,
 ('E', 'C'): -6.9,
...

levin

Value:
{('A', 'A'): 2,
 ('A', 'D'): 0,
 ('A', 'E'): 1,
 ('A', 'G'): 0,
 ('A', 'P'): -1,
 ('C', 'A'): 0,
 ('C', 'C'): 2,
 ('C', 'D'): 0,
...

mclach

Value:
{('A', 'A'): 8,
 ('A', 'F'): 1,
 ('A', 'G'): 3,
 ('A', 'I'): 2,
 ('A', 'L'): 2,
 ('A', 'M'): 3,
 ('A', 'V'): 3,
 ('A', 'W'): 1,
...

miyata

Value:
{('A', 'A'): 1.25,
 ('A', 'C'): -0.14,
 ('A', 'P'): 1.19,
 ('C', 'C'): 1.25,
 ('D', 'A'): -1.12,
 ('D', 'C'): -2.23,
 ('D', 'D'): 1.25,
 ('D', 'E'): 0.35,
...

nwsgappep

Value:
{('A', 'A'): 1.5,
 ('B', 'A'): 0.2,
 ('B', 'B'): 1.1,
 ('C', 'A'): 0.3,
 ('C', 'B'): -0.4,
 ('C', 'C'): 1.5,
 ('D', 'A'): 0.3,
 ('D', 'B'): 1.1,
...

pam120

Value:
{('A', 'A'): 3,
 ('B', 'A'): 0,
 ('B', 'B'): 4,
 ('B', 'C'): -6,
 ('B', 'D'): 4,
 ('B', 'E'): 3,
 ('B', 'F'): -5,
 ('B', 'G'): 0,
...

pam180

Value:
{('A', 'A'): 3,
 ('B', 'A'): 0,
 ('B', 'B'): 4,
 ('B', 'C'): -6,
 ('B', 'D'): 4,
 ('B', 'E'): 3,
 ('B', 'F'): -6,
 ('B', 'G'): 0,
...

pam250

Value:
{('A', 'A'): 2,
 ('B', 'A'): 0,
 ('B', 'B'): 3,
 ('B', 'C'): -4,
 ('B', 'D'): 3,
 ('B', 'E'): 3,
 ('B', 'F'): -4,
 ('B', 'G'): 0,
...

pam30

Value:
{('A', 'A'): 6,
 ('B', 'A'): -3,
 ('B', 'B'): 6,
 ('B', 'C'): -12,
 ('B', 'D'): 6,
 ('B', 'E'): 1,
 ('B', 'F'): -10,
 ('B', 'G'): -3,
...

pam300

Value:
{('A', 'A'): 2,
 ('B', 'A'): 0,
 ('B', 'B'): 3,
 ('B', 'C'): -5,
 ('B', 'D'): 3,
 ('B', 'E'): 3,
 ('B', 'F'): -5,
 ('B', 'G'): 1,
...

pam60

Value:
{('A', 'A'): 5,
 ('B', 'A'): -2,
 ('B', 'B'): 5,
 ('B', 'C'): -9,
 ('B', 'D'): 5,
 ('B', 'E'): 2,
 ('B', 'F'): -8,
 ('B', 'G'): -2,
...

pam90

Value:
{('A', 'A'): 4,
 ('B', 'A'): -1,
 ('B', 'B'): 4,
 ('B', 'C'): -7,
 ('B', 'D'): 5,
 ('B', 'E'): 2,
 ('B', 'F'): -6,
 ('B', 'G'): -1,
...

rao

Value:
{('A', 'A'): 16,
 ('C', 'A'): 11,
 ('C', 'C'): 16,
 ('D', 'A'): 9,
 ('D', 'C'): 8,
 ('D', 'D'): 16,
 ('E', 'A'): 10,
 ('E', 'C'): 9,
...

risler

Value:
{('A', 'A'): 2.2,
 ('C', 'A'): -1.5,
 ('C', 'C'): 2.2,
 ('D', 'A'): 0.2,
 ('D', 'C'): -1.7,
 ('D', 'D'): 2.2,
 ('E', 'A'): 1.7,
 ('E', 'C'): -1.5,
...

structure

Value:
{('A', 'A'): 4,
 ('A', 'C'): -2,
 ('A', 'P'): -1,
 ('A', 'S'): 0,
 ('A', 'T'): -1,
 ('C', 'C'): 11,
 ('D', 'A'): -1,
 ('D', 'C'): -7,
...