X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=resources%2FscoreModel%2Fblosum62.scm;fp=resources%2FscoreModel%2Fblosum62.scm;h=c7af6b0b55e84df3d16715df6252a58fffa2f935;hb=6129931bfa23eec90e6556a4d0412ef34aff5759;hp=3df8833e2a3cc9527372688bfca07b8004e29691;hpb=c6e8e8ccd10f21698226ae37196cd9680e6804a0;p=jalview.git

diff --git a/resources/scoreModel/blosum62.scm b/resources/scoreModel/blosum62.scm
index 3df8833..c7af6b0 100644
--- a/resources/scoreModel/blosum62.scm
+++ b/resources/scoreModel/blosum62.scm
@@ -5,38 +5,39 @@ ARNDCQEGHILKMFPSTWYVBZX *
 # The first line declares a ScoreMatrix with the name BLOSUM62 (shown in menus)
 # The second line gives the symbols for which scores are held in the matrix
 # These may include a space (but not as the first or last character)
-# Scores are not case sensitive, unless column(s) are provided for lower case characters
 #
+# Scores are not symbol case sensitive, unless column(s) are provided for lower case characters
+# The 'guide symbol' at the start of each row of score values is optional
 #
-# Comment line with symbols is provided as a guide
+# Comment header line with symbols is provided as a guide
 # Values may be integer or floating point, delimited by tab, space, comma or combinations
 #
 #	A	R	N	D	C	Q	E	G	H	I	L	K	M	F	P	S	T	W	Y	V	B	Z	X	    *
 #
-	4	-1	-2	-2	0	-1	-1	0	-2	-1	-1	-1	-1	-2	-1	1	0	-3	-2	0	-2	-1	0	-4 -4
-	-1	5	0	-2	-3	1	0	-2	0	-3	-2	2	-1	-3	-2	-1	-1	-3	-2	-3	-1	0	-1	-4 -4
-	-2	0	6	1	-3	0	0	0	1	-3	-3	0	-2	-3	-2	1	0	-4	-2	-3	3	0	-1	-4 -4
-	-2	-2	1	6	-3	0	2	-1	-1	-3	-4	-1	-3	-3	-1	0	-1	-4	-3	-3	4	1	-1	-4 -4
-	0	3	-3	-3	9	-3	-4	-3	-3	-1	-1	-3	-1	-2	-3	-1	-1	-2	-2	-1	-3	-3	-2	-4 -4
-	-1	1	0	0	-3	5	2	-2	0	-3	-2	1	0	-3	-1	0	-1	-2	-1	-2	0	3	-1	-4 -4
-	-1	0	0	2	-4	2	5	-2	0	-3	-3	1	-2	-3	-1	0	-1	-3	-2	-2	1	4	-1	-4 -4
-	0	-2	0	-1	-3	-2	-2	6	-2	-4	-4	-2	-3	-3	-2	0	-2	-2	-3	-3	-1	-2	-1	-4 -4
-	-2	0	1	-1	-3	0	0	-2	8	-3	-3	-1	-2	-1	-2	-1	-2	-2	2	-3	0	0	-1	-4 -4
-	-1	-3	-3	-3	-1	-3	-3	-4	-3	4	2	-3	1	0	-3	-2	-1	-3	-1	3	-3	-3	-1	-4 -4
-	-1	-2	-3	-4	-1	-2	-3	-4	-3	2	4	-2	2	0	-3	-2	-1	-2	-1	1	-4	-3	-1	-4 -4
-	-1	2	0	-1	-3	1	1	-2	-1	-3	-2	5	-1	-3	-1	0	-1	-3	-2	-2	0	1	-1	-4 -4
-	-1	-1	-2	-3	-1	0	-2	-3	-2	1	2	-1	5	0	-2	-1	-1	-1	-1	1	-3	-1	-1	-4 -4
-	-2	-3	-3	-3	-2	-3	-3	-3	-1	0	0	-3	0	6	-4	-2	-2	1	3	-1	-3	-3	-1	-4 -4
-	-1	-2	-2	-1	-3	-1	-1	-2	-2	-3	-3	-1	-2	-4	7	-1	-1	-4	-3	-2	-2	-1	-2	-4 -4
-	1	-1	1	0	-1	0	0	0	-1	-2	-2	0	-1	-2	-1	4	1	-3	-2	-2	0	0	0	-4 -4
-	0	-1	0	-1	-1	-1	-1	-2	-2	-1	-1	-1	-1	-2	-1	1	5	-2	-2	0	-1	-1	0	-4 -4
-	-3	-3	-4	-4	-2	-2	-3	-2	-2	-3	-2	-3	-1	1	-4	-3	-2	11	2	-3	-4	-3	-2	-4 -4
-	-2	-2	-2	-3	-2	-1	-2	-3	2	-1	-1	-2	-1	3	-3	-2	-2	2	7	-1	-3	-2	-1	-4 -4
-	0	-3	-3	-3	-1	-2	-2	-3	-3	3	1	-2	1	-1	-2	-2	0	-3	-1	4	-3	-2	-1	-4 -4
-	-2	-1	3	4	-3	0	1	-1	0	-3	-4	0	-3	-3	-2	0	-1	-4	-3	-3	4	1	-1	-4 -4
-	-1	0	0	1	-3	3	4	-2	0	-3	-3	1	-1	-3	-1	0	-1	-3	-2	-2	1	4	-1	-4 -4
-	0	-1	-1	-1	-2	-1	-1	-1	-1	-1	-1	-1	-1	-1	-2	0	0	-2	-1	-1	-1	-1	-1	-4 -4
-	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	1  1
+A	4	-1	-2	-2	0	-1	-1	0	-2	-1	-1	-1	-1	-2	-1	1	0	-3	-2	0	-2	-1	0	-4 -4
+R	-1	5	0	-2	-3	1	0	-2	0	-3	-2	2	-1	-3	-2	-1	-1	-3	-2	-3	-1	0	-1	-4 -4
+N	-2	0	6	1	-3	0	0	0	1	-3	-3	0	-2	-3	-2	1	0	-4	-2	-3	3	0	-1	-4 -4
+D	-2	-2	1	6	-3	0	2	-1	-1	-3	-4	-1	-3	-3	-1	0	-1	-4	-3	-3	4	1	-1	-4 -4
+C	0	3	-3	-3	9	-3	-4	-3	-3	-1	-1	-3	-1	-2	-3	-1	-1	-2	-2	-1	-3	-3	-2	-4 -4
+Q	-1	1	0	0	-3	5	2	-2	0	-3	-2	1	0	-3	-1	0	-1	-2	-1	-2	0	3	-1	-4 -4
+E	-1	0	0	2	-4	2	5	-2	0	-3	-3	1	-2	-3	-1	0	-1	-3	-2	-2	1	4	-1	-4 -4
+G	0	-2	0	-1	-3	-2	-2	6	-2	-4	-4	-2	-3	-3	-2	0	-2	-2	-3	-3	-1	-2	-1	-4 -4
+H	-2	0	1	-1	-3	0	0	-2	8	-3	-3	-1	-2	-1	-2	-1	-2	-2	2	-3	0	0	-1	-4 -4
+I	-1	-3	-3	-3	-1	-3	-3	-4	-3	4	2	-3	1	0	-3	-2	-1	-3	-1	3	-3	-3	-1	-4 -4
+L	-1	-2	-3	-4	-1	-2	-3	-4	-3	2	4	-2	2	0	-3	-2	-1	-2	-1	1	-4	-3	-1	-4 -4
+K	-1	2	0	-1	-3	1	1	-2	-1	-3	-2	5	-1	-3	-1	0	-1	-3	-2	-2	0	1	-1	-4 -4
+M	-1	-1	-2	-3	-1	0	-2	-3	-2	1	2	-1	5	0	-2	-1	-1	-1	-1	1	-3	-1	-1	-4 -4
+F	-2	-3	-3	-3	-2	-3	-3	-3	-1	0	0	-3	0	6	-4	-2	-2	1	3	-1	-3	-3	-1	-4 -4
+P	-1	-2	-2	-1	-3	-1	-1	-2	-2	-3	-3	-1	-2	-4	7	-1	-1	-4	-3	-2	-2	-1	-2	-4 -4
+S	1	-1	1	0	-1	0	0	0	-1	-2	-2	0	-1	-2	-1	4	1	-3	-2	-2	0	0	0	-4 -4
+T	0	-1	0	-1	-1	-1	-1	-2	-2	-1	-1	-1	-1	-2	-1	1	5	-2	-2	0	-1	-1	0	-4 -4
+W	-3	-3	-4	-4	-2	-2	-3	-2	-2	-3	-2	-3	-1	1	-4	-3	-2	11	2	-3	-4	-3	-2	-4 -4
+Y	-2	-2	-2	-3	-2	-1	-2	-3	2	-1	-1	-2	-1	3	-3	-2	-2	2	7	-1	-3	-2	-1	-4 -4
+V	0	-3	-3	-3	-1	-2	-2	-3	-3	3	1	-2	1	-1	-2	-2	0	-3	-1	4	-3	-2	-1	-4 -4
+B	-2	-1	3	4	-3	0	1	-1	0	-3	-4	0	-3	-3	-2	0	-1	-4	-3	-3	4	1	-1	-4 -4
+Z	-1	0	0	1	-3	3	4	-2	0	-3	-3	1	-1	-3	-1	0	-1	-3	-2	-2	1	4	-1	-4 -4
+X	0	-1	-1	-1	-2	-1	-1	-1	-1	-1	-1	-1	-1	-1	-2	0	0	-2	-1	-1	-1	-1	-1	-4 -4
 	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	1  1
+*	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	1  1
 #
 #	A	R	N	D	C	Q	E	G	H	I	L	K	M	F	P	S	T	W	Y	V	B	Z	X	*