r27269 - /trunk/lib/sequence_alignment/substitution_matrices.py -- January 22, 2015 - 16:35

Author: bugman
Date: Thu Jan 22 16:35:49 2015
New Revision: 27269

URL: http://svn.gna.org/viewcvs/relax?rev=27269&view=rev
Log:
Added the header from ftp://ftp.ncbi.nih.gov/blast/matrices/BLOSUM62.

This is to document the BLOSUM62 substitution matrix.


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=27269&r1=27268&r2=27269&view=diff
==============================================================================
--- trunk/lib/sequence_alignment/substitution_matrices.py       (original)
+++ trunk/lib/sequence_alignment/substitution_matrices.py       Thu Jan 22 
16:35:49 2015
@@ -65,6 +65,14 @@
 ], int16)
 
 
+#  Matrix made by matblas from blosum62.iij
+#  * column uses minimum score
+#  BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
+#  Blocks Database = /data/blocks_5.0/blocks.dat
+#  Cluster Percentage: >= 62
+#  Entropy =   0.6979, Expected =  -0.5209
+#
+# Taken from ftp://ftp.ncbi.nih.gov/blast/matrices/BLOSUM62.
 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,  *