Back to index

python-biopython  1.60
Functions | Variables
Bio.SubsMat.MatrixInfo Namespace Reference

Functions

def _temp

Variables

list available_matrices
tuple benner6 = _temp()
tuple benner22 = _temp()
tuple benner74 = _temp()
tuple blosum100 = _temp()
tuple blosum30 = _temp()
tuple blosum35 = _temp()
tuple blosum40 = _temp()
tuple blosum45 = _temp()
tuple blosum50 = _temp()
tuple blosum55 = _temp()
tuple blosum60 = _temp()
tuple blosum62 = _temp()
tuple blosum65 = _temp()
tuple blosum70 = _temp()
tuple blosum75 = _temp()
tuple blosum80 = _temp()
tuple blosum85 = _temp()
tuple blosum90 = _temp()
tuple blosum95 = _temp()
tuple feng = _temp()
tuple fitch = _temp()
tuple genetic = _temp()
tuple gonnet = _temp()
tuple grant = _temp()
tuple ident = _temp()
tuple johnson = _temp()
tuple levin = _temp()
tuple mclach = _temp()
tuple miyata = _temp()
tuple nwsgappep = _temp()
tuple pam120 = _temp()
tuple pam180 = _temp()
tuple pam250 = _temp()
tuple pam30 = _temp()
tuple pam300 = _temp()
tuple pam60 = _temp()
tuple pam90 = _temp()
tuple rao = _temp()
tuple risler = _temp()
tuple structure = _temp()

Detailed Description

A whole bunch of substitution matrices for use in alignments, etc.

The info on this page was obtained from:
    http://www.embl-heidelberg.de/~vogt/matrices/mlist1.html
and was extracted using the code in 'get_matrices.py.'

Function Documentation

def Bio.SubsMat.MatrixInfo._temp ( ) [private]

Definition at line 28 of file MatrixInfo.py.

00028 
00029 def _temp():
00030     return {
00031 ('W', 'F') : -1.6, ('L', 'R') : -3.2, ('I', 'I') : 4.4, ('Q', 'Q') : 5.3, 
00032 ('W', 'N') : -4.4, ('V', 'I') : 3.9, ('H', 'T') : -1.7, ('H', 'P') : -0.4, 
00033 ('W', 'V') : -4.8, ('Q', 'E') : 2.1, ('W', 'R') : 2.0, ('Q', 'A') : -1.7, 
00034 ('H', 'H') : 6.1, ('H', 'D') : 0.1, ('L', 'N') : -3.4, ('Y', 'M') : -3.6, 
00035 ('Y', 'I') : -3.3, ('Y', 'E') : -4.1, ('E', 'S') : -1.2, ('Y', 'A') : -4.0, 
00036 ('Y', 'Y') : 9.5, ('T', 'C') : -1.5, ('E', 'C') : -4.7, ('Y', 'Q') : -1.4, 
00037 ('E', 'G') : 0.5, ('V', 'A') : 0.7, ('C', 'C') : 12.1, ('M', 'R') : -3.0, 
00038 ('P', 'T') : 0.6, ('V', 'E') : -3.0, ('P', 'P') : 6.5, ('I', 'T') : 0.7, 
00039 ('K', 'S') : -1.2, ('R', 'G') : -0.1, ('I', 'P') : -2.0, ('R', 'C') : -0.4, 
00040 ('A', 'T') : 1.7, ('K', 'K') : 5.6, ('A', 'P') : 1.1, ('V', 'M') : 3.3, 
00041 ('I', 'D') : -4.2, ('K', 'C') : -2.8, ('K', 'G') : -1.4, ('R', 'S') : -0.9, 
00042 ('F', 'Q') : -4.4, ('F', 'A') : -3.2, ('V', 'V') : 4.0, ('M', 'N') : -2.5, 
00043 ('F', 'E') : -6.7, ('D', 'N') : 2.5, ('F', 'I') : 0.0, ('F', 'M') : -0.1, 
00044 ('M', 'S') : -1.3, ('S', 'S') : 2.1, ('L', 'Q') : -2.4, ('W', 'E') : -5.6, 
00045 ('W', 'A') : -4.3, ('W', 'M') : -4.4, ('H', 'S') : -0.9, ('W', 'I') : -5.0, 
00046 ('S', 'C') : 0.9, ('L', 'A') : -1.3, ('L', 'E') : -5.0, ('W', 'Q') : -2.6, 
00047 ('H', 'G') : -2.1, ('Q', 'N') : 0.1, ('H', 'C') : -1.2, ('L', 'M') : -2.9, 
00048 ('W', 'Y') : -0.3, ('Y', 'N') : -0.9, ('E', 'P') : -2.6, ('Y', 'F') : 5.6, 
00049 ('E', 'T') : -1.6, ('A', 'A') : 2.5, ('I', 'N') : -2.5, ('G', 'A') : 0.8, 
00050 ('Y', 'V') : -3.8, ('E', 'D') : 4.4, ('W', 'H') : -2.8, ('Y', 'R') : -2.6, 
00051 ('M', 'Q') : -3.1, ('P', 'S') : 1.4, ('R', 'H') : 1.8, ('A', 'C') : -1.7, 
00052 ('R', 'D') : -1.5, ('K', 'P') : -2.3, ('L', 'D') : -5.3, ('K', 'T') : -1.1, 
00053 ('V', 'N') : -2.4, ('M', 'A') : -0.2, ('K', 'H') : 0.9, ('V', 'R') : -3.7, 
00054 ('P', 'C') : -2.7, ('M', 'E') : -4.1, ('A', 'S') : 1.4, ('T', 'T') : 2.4, 
00055 ('R', 'T') : -1.3, ('I', 'G') : -3.4, ('R', 'P') : -1.3, ('K', 'D') : -0.2, 
00056 ('I', 'C') : -3.6, ('F', 'R') : -4.9, ('F', 'V') : -0.5, ('L', 'C') : -3.8, 
00057 ('F', 'F') : 8.3, ('D', 'A') : -0.6, ('F', 'N') : -3.5, ('W', 'D') : -6.3, 
00058 ('L', 'P') : -0.2, ('Q', 'S') : -1.4, ('N', 'C') : -1.6, ('N', 'G') : -0.1, 
00059 ('H', 'N') : 1.4, ('W', 'T') : -2.6, ('Q', 'G') : -1.6, ('W', 'P') : -4.8, 
00060 ('Q', 'C') : -3.2, ('N', 'S') : 1.2, ('L', 'H') : -2.2, ('L', 'L') : 4.8, 
00061 ('G', 'T') : -0.5, ('M', 'M') : 4.8, ('G', 'P') : -1.7, ('Y', 'K') : -4.0, 
00062 ('Y', 'G') : -4.9, ('Y', 'C') : 2.6, ('E', 'A') : -0.7, ('E', 'E') : 5.2, 
00063 ('Y', 'S') : -1.8, ('M', 'P') : -1.8, ('V', 'C') : -3.1, ('M', 'T') : 0.6, 
00064 ('V', 'G') : -2.3, ('R', 'E') : -0.4, ('V', 'K') : -3.8, ('K', 'Q') : 2.5, 
00065 ('R', 'A') : -1.7, ('I', 'R') : -3.8, ('N', 'A') : 0.0, ('V', 'S') : -0.9, 
00066 ('M', 'D') : -4.3, ('M', 'H') : -3.4, ('K', 'A') : -1.9, ('R', 'Q') : 2.5, 
00067 ('K', 'E') : 0.9, ('F', 'S') : -1.8, ('I', 'K') : -3.8, ('D', 'P') : -2.8, 
00068 ('D', 'T') : -1.2, ('I', 'M') : 4.0, ('F', 'C') : -0.1, ('W', 'L') : -3.0, 
00069 ('F', 'G') : -5.7, ('F', 'K') : -6.3, ('F', 'T') : -2.4, ('D', 'D') : 5.2, 
00070 ('Q', 'T') : -1.7, ('W', 'G') : -1.7, ('Q', 'P') : 0.1, ('W', 'C') : 1.6, 
00071 ('W', 'K') : -1.4, ('H', 'Q') : 3.2, ('Q', 'D') : 0.6, ('W', 'W') : 14.7, 
00072 ('V', 'L') : 1.9, ('L', 'G') : -4.6, ('W', 'S') : -2.9, ('L', 'K') : -4.1, 
00073 ('N', 'P') : -1.1, ('H', 'E') : -0.2, ('N', 'T') : 0.5, ('H', 'A') : -2.1, 
00074 ('Y', 'L') : -1.6, ('Y', 'H') : 4.4, ('G', 'S') : 0.8, ('Y', 'D') : -2.3, 
00075 ('V', 'Q') : -3.5, ('L', 'T') : -0.4, ('G', 'G') : 5.8, ('G', 'C') : -1.3, 
00076 ('E', 'N') : 1.1, ('Y', 'T') : -3.4, ('Y', 'P') : -3.8, ('R', 'N') : -0.1, 
00077 ('V', 'D') : -3.3, ('K', 'R') : 4.3, ('V', 'H') : -3.8, ('I', 'Q') : -3.8, 
00078 ('V', 'P') : -1.6, ('M', 'C') : -3.7, ('K', 'N') : 1.0, ('V', 'T') : 0.6, 
00079 ('M', 'G') : -3.7, ('T', 'S') : 1.5, ('I', 'E') : -4.1, ('M', 'K') : -2.9, 
00080 ('I', 'A') : 0.1, ('N', 'N') : 3.6, ('R', 'R') : 5.1, ('F', 'P') : -3.2, 
00081 ('L', 'I') : 2.4, ('I', 'S') : -1.2, ('D', 'S') : -0.4, ('L', 'S') : -1.5, 
00082 ('I', 'H') : -3.7, ('F', 'D') : -5.7, ('D', 'C') : -3.7, ('F', 'H') : 0.1, 
00083 ('D', 'G') : 0.8, ('F', 'L') : 2.4
}

Variable Documentation

Initial value:
00001 ['benner6', 'benner22', 'benner74', 'blosum100',
00002                       'blosum30', 'blosum35', 'blosum40', 'blosum45', 
00003                       'blosum50', 'blosum55', 'blosum60', 'blosum62', 
00004                       'blosum65', 'blosum70', 'blosum75', 'blosum80', 
00005                       'blosum85', 'blosum90', 'blosum95', 'feng', 
00006                       'fitch', 'genetic', 'gonnet', 'grant', 
00007                       'ident', 'johnson', 'levin', 'mclach', 
00008                       'miyata', 'nwsgappep', 'pam120', 'pam180', 
00009                       'pam250', 'pam30', 'pam300', 'pam60', 
00010                       'pam90', 'rao', 'risler', 'structure'
00011                      ]

Definition at line 9 of file MatrixInfo.py.

Definition at line 143 of file MatrixInfo.py.

Definition at line 84 of file MatrixInfo.py.

Definition at line 204 of file MatrixInfo.py.

Definition at line 281 of file MatrixInfo.py.

Definition at line 358 of file MatrixInfo.py.

Definition at line 435 of file MatrixInfo.py.

Definition at line 512 of file MatrixInfo.py.

Definition at line 589 of file MatrixInfo.py.

Definition at line 666 of file MatrixInfo.py.

Definition at line 743 of file MatrixInfo.py.

Definition at line 820 of file MatrixInfo.py.

Definition at line 897 of file MatrixInfo.py.

Definition at line 974 of file MatrixInfo.py.

Definition at line 1051 of file MatrixInfo.py.

Definition at line 1128 of file MatrixInfo.py.

Definition at line 1205 of file MatrixInfo.py.

Definition at line 1282 of file MatrixInfo.py.

Definition at line 1359 of file MatrixInfo.py.

Definition at line 1436 of file MatrixInfo.py.

Definition at line 1497 of file MatrixInfo.py.

Definition at line 1548 of file MatrixInfo.py.

Definition at line 1609 of file MatrixInfo.py.

Definition at line 1670 of file MatrixInfo.py.

Definition at line 1731 of file MatrixInfo.py.

Definition at line 1792 of file MatrixInfo.py.

Definition at line 1853 of file MatrixInfo.py.

Definition at line 1915 of file MatrixInfo.py.

Definition at line 1976 of file MatrixInfo.py.

Definition at line 2037 of file MatrixInfo.py.

Definition at line 2108 of file MatrixInfo.py.

Definition at line 2185 of file MatrixInfo.py.

Definition at line 2262 of file MatrixInfo.py.

Definition at line 2339 of file MatrixInfo.py.

Definition at line 2416 of file MatrixInfo.py.

Definition at line 2493 of file MatrixInfo.py.

Definition at line 2570 of file MatrixInfo.py.

Definition at line 2642 of file MatrixInfo.py.

Definition at line 2703 of file MatrixInfo.py.

Definition at line 2764 of file MatrixInfo.py.

Definition at line 2825 of file MatrixInfo.py.