X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=resources%2FscoreModel%2Fdna.scm;h=0d7cbc102a730490c604f99ba7bf5872a63f7874;hb=2c1fabdc3d0b711ebcc844c846fefa61d4e58bd8;hp=d32647b6af03f1dc545bc13c93c57127e0a38e8b;hpb=73a369b0c2d5991400985d533107b70450b3d613;p=jalview.git

diff --git a/resources/scoreModel/dna.scm b/resources/scoreModel/dna.scm
index d32647b..0d7cbc1 100644
--- 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