X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=resources%2FscoreModel%2Fdna.scm;fp=resources%2FscoreModel%2Fdna.scm;h=e66864a89a4a436f8f66f72af5f636eaab6327d8;hb=613a7a5d1fe2758f0bb620e49eeb87fa45b5458f;hp=d32647b6af03f1dc545bc13c93c57127e0a38e8b;hpb=efa724edf32b5803396087cf7c94521e3d597836;p=jalview.git

diff --git a/resources/scoreModel/dna.scm b/resources/scoreModel/dna.scm
index d32647b..e66864a 100644
--- a/resources/scoreModel/dna.scm
+++ b/resources/scoreModel/dna.scm
@@ -1,5 +1,5 @@
 ScoreMatrix DNA
-ACGTUIXRYN -
+ACGTUIXRYN-
 #
 # A DNA substitution matrix.
 # This is an ad-hoc matrix which, in addition to penalising mutations between the common 
@@ -10,26 +10,21 @@ 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	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
 #
 #	A	C	G	T	U	I	X	R	Y	N		-