From c8588db8a405d69734772266f2ad824b5ee976f4 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Mon, 27 Mar 2017 19:13:20 +0100 Subject: [PATCH 1/1] JAL-2416 amended to (as near as possible) strict NCBI format --- resources/scoreModel/blosum62.scm | 2 -- resources/scoreModel/dna.scm | 1 - resources/scoreModel/pam250.scm | 3 +-- 3 files changed, 1 insertion(+), 5 deletions(-) diff --git a/resources/scoreModel/blosum62.scm b/resources/scoreModel/blosum62.scm index b793e04..50e74cc 100644 --- a/resources/scoreModel/blosum62.scm +++ b/resources/scoreModel/blosum62.scm @@ -1,5 +1,4 @@ ScoreMatrix BLOSUM62 -ARNDCQEGHILKMFPSTWYVBZX-* # # 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) @@ -9,7 +8,6 @@ ARNDCQEGHILKMFPSTWYVBZX-* # 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 -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 -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 -4 diff --git a/resources/scoreModel/dna.scm b/resources/scoreModel/dna.scm index e66864a..c490931 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 diff --git a/resources/scoreModel/pam250.scm b/resources/scoreModel/pam250.scm index 05404d0..57922a4 100644 --- a/resources/scoreModel/pam250.scm +++ b/resources/scoreModel/pam250.scm @@ -1,12 +1,11 @@ ScoreMatrix PAM250 -ARNDCQEGHILKMFPSTWYVBZX-* # # The PAM250 substitution matrix # The first line declares a ScoreMatrix with the name PAM250 (shown in menus) # Scores are not case sensitive, unless column(s) are provided for lower case characters # 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 R N D C Q E G H I L K M F P S T W Y V B Z X - * A 2 -2 0 0 -2 0 0 1 -1 -1 -2 -1 -1 -3 1 1 1 -6 -3 0 0 0 0 -8 -8 R -2 6 0 -1 -4 1 -1 -3 2 -2 -3 3 0 -4 0 0 -1 2 -4 -2 -1 0 -1 -8 -8 N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -3 0 1 0 -4 -2 -2 2 1 0 -8 -8 -- 1.7.10.2