JAL-4020 Added path search for global installation path and older version installatio...

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

diff --git a/resources/scoreModel/dna.scm b/resources/scoreModel/dna.scm
index d32647b..0d7cbc1 100644 (file)
--- a/resources/scoreModel/dna.scm
+++ b/resources/scoreModel/dna.scm
@@ -1,5 +1,4 @@
 ScoreMatrix DNA
-ACGTUIXRYN -
 #
 # A DNA substitution matrix.
 # This is an ad-hoc matrix which, in addition to penalising mutations between the common 
@@ -10,26 +9,19 @@ ACGTUIXRYN -
 # any of (ACGTU), and unfavourably match each other.
 #
 # The first line declares a ScoreMatrix with the name DNA (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
 #
-#
-# Header line with symbols is provided as a guide
 # Values may be integer or floating point, delimited by tab, space, comma or combinations
 #
-       A       C       G       T       U       I       X       R       Y       N               -
-       10      -8      -8      -8      -8      1       1       1       -8      1       1       1 
-       -8      10      -8      -8      -8      1       1       -8      1       1       1       1
-       -8      -8      10      -8      -8      1       1       1       -8      1       1       1
-       -8      -8      -8      10      10      1       1       -8      1       1       1       1
-       -8      -8      -8      10      10      1       1       -8      1       1       1       1
-       1       1       1       1       1       10      0       0       0       1       1       1
-       1       1       1       1       1       0       10      0       0       1       1       1
-       1       -8      1       -8      -8      0       0       10      -8      1       1       1
-       -8      1       -8      1       1       0       0       -8      10      1       1       1
-       1       1       1       1       1       1       1       1       1       10      1       1
-       1       1       1       1       1       1       1       1       1       1       1       1
-       1       1       1       1       1       1       1       1       1       1       1       1
-#
-#      A       C       G       T       U       I       X       R       Y       N               -
+        A       C       G       T       U       I       X       R       Y       N      -
+A      10      -8      -8      -8      -8       1       1       1      -8       1      1 
+C      -8      10      -8      -8      -8       1       1      -8       1       1      1
+G      -8      -8      10      -8      -8       1       1       1      -8       1      1
+T      -8      -8      -8      10      10       1       1      -8       1       1      1
+U      -8      -8      -8      10      10       1       1      -8       1       1      1
+I       1       1       1       1       1      10       0       0       0       1      1
+X       1       1       1       1       1       0      10       0       0       1      1
+R       1      -8       1      -8      -8       0       0      10      -8       1      1
+Y      -8       1      -8       1       1       0       0      -8      10       1      1
+N       1       1       1       1       1       1       1       1       1      10      1
+-       1       1       1       1       1       1       1       1       1       1      1