r27266 - /trunk/lib/sequence_alignment/substitution_matrices.py -- January 22, 2015 - 16:01

Author: bugman
Date: Thu Jan 22 16:01:39 2015
New Revision: 27266

URL: http://svn.gna.org/viewcvs/relax?rev=27266&view=rev
Log:
Added a DNA similarity matrix to lib.sequence_alignment.substitution_matrices.


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=27266&r1=27265&r2=27266&view=diff
==============================================================================
--- trunk/lib/sequence_alignment/substitution_matrices.py       (original)
+++ trunk/lib/sequence_alignment/substitution_matrices.py       Thu Jan 22 
16:01:39 2015
@@ -25,6 +25,14 @@
 # Python module imports.
 from numpy import array, int16
 
+
+SIMILARITY_DNA_SEQ = 'AGCT'
+SIMILARITY_DNA = array([
+    [ 1, -1, -1, -1],
+    [-1,  1, -1, -1],
+    [-1, -1,  1, -1],
+    [-1, -1, -1,  1]
+], int16)
 
 BLOSUM62_SEQ = 'ARNDCQEGHILKMFPSTWYVBZX*'
 BLOSUM62 = array([