X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=resources%2FscoreModel%2Fblosum62.scm;fp=resources%2FscoreModel%2Fblosum62.scm;h=b0e927d38fb36e8d318637d0a7f1bcc6ab26a81a;hb=e0aacff0a162fdf1beb71cd5965b6ff4f8c9de0d;hp=0000000000000000000000000000000000000000;hpb=627a783b3535fc5ac2a2b2354ee3f61006f6c37f;p=jalview.git

diff --git a/resources/scoreModel/blosum62.scm b/resources/scoreModel/blosum62.scm
new file mode 100644
index 0000000..b0e927d
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+++ b/resources/scoreModel/blosum62.scm
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+ScoreMatrix BLOSUM62
+#
+# 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)
+#
+# 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
+# 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	 4	-1	-2	-2	 0	-1	-1	 0	-2	-1	-1	-1	-1	-2	-1	 1	 0	-3	-2	 0	-2	-1	 0	-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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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
+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	 1