JAL-2393 example (unvalidated) blosum80 matrix to play with drag and

[jalview.git] / resources / scoreModel / blosum80.scm

diff --git a/resources/scoreModel/blosum80.scm b/resources/scoreModel/blosum80.scm
new file mode 100644 (file)
index 0000000..8de04b7
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+++ b/resources/scoreModel/blosum80.scm
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+ScoreMatrix BLOSUM80
+ARNDCQEGHILKMFPSTWYVBJZX*
+#
+# Source: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/data/BLOSUM80
+#
+# ** THIS IS A SUGGESTED FILE, NOT VALIDATED **
+# Please read https://www.biostars.org/p/190004/ for possible alternatives!
+#
+# The first line declares a ScoreMatrix with the name BLOSUM80
+# 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
+#
+# 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       J       Z       X        *
+A      5       -2      -2      -2      -1      -1      -1      0       -2      -2      -2      -1      -1      -3      -1      1       0       -3      -2      0       -2      -2      -1      -1      -6
+R      -2      6       -1      -2      -4      1       -1      -3      0       -3      -3      2       -2      -4      -2      -1      -1      -4      -3      -3      -1      -3      0       -1      -6
+N      -2      -1      6       1       -3      0       -1      -1      0       -4      -4      0       -3      -4      -3      0       0       -4      -3      -4      5       -4      0       -1      -6
+D      -2      -2      1       6       -4      -1      1       -2      -2      -4      -5      -1      -4      -4      -2      -1      -1      -6      -4      -4      5       -5      1       -1      -6
+C      -1      -4      -3      -4      9       -4      -5      -4      -4      -2      -2      -4      -2      -3      -4      -2      -1      -3      -3      -1      -4      -2      -4      -1      -6
+Q      -1      1       0       -1      -4      6       2       -2      1       -3      -3      1       0       -4      -2      0       -1      -3      -2      -3      0       -3      4       -1      -6
+E      -1      -1      -1      1       -5      2       6       -3      0       -4      -4      1       -2      -4      -2      0       -1      -4      -3      -3      1       -4      5       -1      -6
+G      0       -3      -1      -2      -4      -2      -3      6       -3      -5      -4      -2      -4      -4      -3      -1      -2      -4      -4      -4      -1      -5      -3      -1      -6
+H      -2      0       0       -2      -4      1       0       -3      8       -4      -3      -1      -2      -2      -3      -1      -2      -3      2       -4      -1      -4      0       -1      -6
+I      -2      -3      -4      -4      -2      -3      -4      -5      -4      5       1       -3      1       -1      -4      -3      -1      -3      -2      3       -4      3       -4      -1      -6
+L      -2      -3      -4      -5      -2      -3      -4      -4      -3      1       4       -3      2       0       -3      -3      -2      -2      -2      1       -4      3       -3      -1      -6
+K      -1      2       0       -1      -4      1       1       -2      -1      -3      -3      5       -2      -4      -1      -1      -1      -4      -3      -3      -1      -3      1       -1      -6
+M      -1      -2      -3      -4      -2      0       -2      -4      -2      1       2       -2      6       0       -3      -2      -1      -2      -2      1       -3      2       -1      -1      -6
+F      -3      -4      -4      -4      -3      -4      -4      -4      -2      -1      0       -4      0       6       -4      -3      -2      0       3       -1      -4      0       -4      -1      -6
+P      -1      -2      -3      -2      -4      -2      -2      -3      -3      -4      -3      -1      -3      -4      8       -1      -2      -5      -4      -3      -2      -4      -2      -1      -6
+S      1       -1      0       -1      -2      0       0       -1      -1      -3      -3      -1      -2      -3      -1      5       1       -4      -2      -2      0       -3      0       -1      -6
+T      0       -1      0       -1      -1      -1      -1      -2      -2      -1      -2      -1      -1      -2      -2      1       5       -4      -2      0       -1      -1      -1      -1      -6
+W      -3      -4      -4      -6      -3      -3      -4      -4      -3      -3      -2      -4      -2      0       -5      -4      -4      11      2       -3      -5      -3      -3      -1      -6
+Y      -2      -3      -3      -4      -3      -2      -3      -4      2       -2      -2      -3      -2      3       -4      -2      -2      2       7       -2      -3      -2      -3      -1      -6
+V      0       -3      -4      -4      -1      -3      -3      -4      -4      3       1       -3      1       -1      -3      -2      0       -3      -2      4       -4      2       -3      -1      -6
+B      -2      -1      5       5       -4      0       1       -1      -1      -4      -4      -1      -3      -4      -2      0       -1      -5      -3      -4      5       -4      0       -1      -6
+J      -2      -3      -4      -5      -2      -3      -4      -5      -4      3       3       -3      2       0       -4      -3      -1      -3      -2      2       -4      3       -3      -1      -6
+Z      -1      0       0       1       -4      4       5       -3      0       -4      -3      1       -1      -4      -2      0       -1      -3      -3      -3      0       -3      5       -1      -6
+X      -1      -1      -1      -1      -1      -1      -1      -1      -1      -1      -1      -1      -1      -1      -1      -1      -1      -1      -1      -1      -1      -1      -1      -1      -6
+*      -6      -6      -6      -6      -6      -6      -6      -6      -6      -6      -6      -6      -6      -6      -6      -6      -6      -6      -6      -6      -6      -6      -6      -6      1
+#
+#      A       R       N       D       C       Q       E       G       H       I       L       K       M       F       P       S       T       W       Y       V       B       J       Z       X       *