JAL-2416 amended to (as near as possible) strict NCBI format

[jalview.git] / resources / scoreModel / blosum62.scm

diff --git a/resources/scoreModel/blosum62.scm b/resources/scoreModel/blosum62.scm
index 5bb1b53..50e74cc 100644 (file)
--- a/resources/scoreModel/blosum62.scm
+++ b/resources/scoreModel/blosum62.scm
@@ -1,24 +1,18 @@
 ScoreMatrix BLOSUM62
-ARNDCQEGHILKMFPSTWYVBZX *
 #
 # The BLOSUM62 substitution matrix, as at https://www.ncbi.nlm.nih.gov/Class/FieldGuide/BLOSUM62.txt
 # 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 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
-#
-# Header line with symbols may be 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           *
-#
+       A       R       N       D       C       Q       E       G       H       I       L       K       M       F       P       S       T       W       Y       V       B       Z       X       -   *
 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
+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
@@ -37,7 +31,7 @@ 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
 *      -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       *