r27268 - /trunk/lib/sequence_alignment/substitution_matrices.py -- January 22, 2015 - 16:34

Author: bugman
Date: Thu Jan 22 16:34:06 2015
New Revision: 27268

URL: http://svn.gna.org/viewcvs/relax?rev=27268&view=rev
Log:
Added the NUC 4.4 nucleotide substitution matrix from 
ftp://ftp.ncbi.nih.gov/blast/matrices/.

Uracil was added to the table as a copy to T.


Modified:
    trunk/lib/sequence_alignment/substitution_matrices.py

Modified: trunk/lib/sequence_alignment/substitution_matrices.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/lib/sequence_alignment/substitution_matrices.py?rev=27268&r1=27267&r2=27268&view=diff
==============================================================================
--- trunk/lib/sequence_alignment/substitution_matrices.py       (original)
+++ trunk/lib/sequence_alignment/substitution_matrices.py       Thu Jan 22 
16:34:06 2015
@@ -34,6 +34,37 @@
     [-1, -1, -1,  1]
 ], int16)
 
+
+# This matrix was created by Todd Lowe   12/10/92
+#
+# Uses ambiguous nucleotide codes, probabilities rounded to
+#  nearest integer
+#
+# Lowest score = -4, Highest score = 5
+#
+# Taken from ftp://ftp.ncbi.nih.gov/blast/matrices/NUC.4.4.
+NUC_4_4_SEQ = 'ATGCSWRYKMBVHDNU'
+NUC_4_4 = array([
+    # A,   T,   G,   C,   S,   W,   R,   Y,   K,   M,   B,   V,   H,   D,   
N,   U
+    [ 5,  -4,  -4,  -4,  -4,   1,   1,  -4,  -4,   1,  -4,  -1,  -1,  -1,  
-2,  -4],  # A
+    [-4,   5,  -4,  -4,  -4,   1,  -4,   1,   1,  -4,  -1,  -4,  -1,  -1,  
-2,   5],  # T
+    [-4,  -4,   5,  -4,   1,  -4,   1,  -4,   1,  -4,  -1,  -1,  -4,  -1,  
-2,  -4],  # G
+    [-4,  -4,  -4,   5,   1,  -4,  -4,   1,  -4,   1,  -1,  -1,  -1,  -4,  
-2,  -4],  # C
+    [-4,  -4,   1,   1,  -1,  -4,  -2,  -2,  -2,  -2,  -1,  -1,  -3,  -3,  
-1,  -4],  # S
+    [ 1,   1,  -4,  -4,  -4,  -1,  -2,  -2,  -2,  -2,  -3,  -3,  -1,  -1,  
-1,   1],  # W
+    [ 1,  -4,   1,  -4,  -2,  -2,  -1,  -4,  -2,  -2,  -3,  -1,  -3,  -1,  
-1,  -4],  # R
+    [-4,   1,  -4,   1,  -2,  -2,  -4,  -1,  -2,  -2,  -1,  -3,  -1,  -3,  
-1,   1],  # Y
+    [-4,   1,   1,  -4,  -2,  -2,  -2,  -2,  -1,  -4,  -1,  -3,  -3,  -1,  
-1,   1],  # K
+    [ 1,  -4,  -4,   1,  -2,  -2,  -2,  -2,  -4,  -1,  -3,  -1,  -1,  -3,  
-1,  -4],  # M
+    [-4,  -1,  -1,  -1,  -1,  -3,  -3,  -1,  -1,  -3,  -1,  -2,  -2,  -2,  
-1,  -1],  # B
+    [-1,  -4,  -1,  -1,  -1,  -3,  -1,  -3,  -3,  -1,  -2,  -1,  -2,  -2,  
-1,  -4],  # V
+    [-1,  -1,  -4,  -1,  -3,  -1,  -3,  -1,  -3,  -1,  -2,  -2,  -1,  -2,  
-1,  -1],  # H
+    [-1,  -1,  -1,  -4,  -3,  -1,  -1,  -3,  -1,  -3,  -2,  -2,  -2,  -1,  
-1,  -1],  # D
+    [-2,  -2,  -2,  -2,  -1,  -1,  -1,  -1,  -1,  -1,  -1,  -1,  -1,  -1,  
-1,  -2],  # N
+    [-4,   5,  -4,  -4,  -4,   1,  -4,   1,   1,  -4,  -1,  -4,  -1,  -1,  
-2,   5],  # U
+], int16)
+
+
 BLOSUM62_SEQ = 'ARNDCQEGHILKMFPSTWYVBZX*'
 BLOSUM62 = array([
     # A,  R,  N,  D,  C,  Q,  E,  G,  H,  I,  L,  K,  M,  F,  P,  S,  T,  W, 
 Y,  V,  B,  Z,  X,  *