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, *
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