From cb96e9aeefe2db534ba45dff656b978839c45646 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Mon, 27 Mar 2017 19:13:44 +0100 Subject: [PATCH 1/1] JAL-2416 amended to AAindex format --- resources/scoreModel/blosum80.scm | 74 +++++++++++++++---------------------- 1 file changed, 30 insertions(+), 44 deletions(-) diff --git a/resources/scoreModel/blosum80.scm b/resources/scoreModel/blosum80.scm index 8de04b7..8153d3b 100644 --- a/resources/scoreModel/blosum80.scm +++ b/resources/scoreModel/blosum80.scm @@ -1,46 +1,32 @@ -ScoreMatrix BLOSUM80 -ARNDCQEGHILKMFPSTWYVBJZX* # -# Source: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/data/BLOSUM80 +# Source: http://www.genome.jp/dbget-bin/www_bget?aaindex:HENS920103 # -# ** 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 * +H HENS920103 +D BLOSUM80 substitution matrix (Henikoff-Henikoff, 1992) +R PMID:1438297 +A Henikoff, S. and Henikoff, J.G. +T Amino acid substitution matrices from protein blocks +J Proc. Natl. Acad. Sci. USA 89, 10915-10919 (1992) +* matrix in 1/3 Bit Units +M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV + 7. + -3. 9. + -3. -1. 9. + -3. -3. 2. 10. + -1. -6. -5. -7. 13. + -2. 1. 0. -1. -5. 9. + -2. -1. -1. 2. -7. 3. 8. + 0. -4. -1. -3. -6. -4. -4. 9. + -3. 0. 1. -2. -7. 1. 0. -4. 12. + -3. -5. -6. -7. -2. -5. -6. -7. -6. 7. + -3. -4. -6. -7. -3. -4. -6. -7. -5. 2. 6. + -1. 3. 0. -2. -6. 2. 1. -3. -1. -5. -4. 8. + -2. -3. -4. -6. -3. -1. -4. -5. -4. 2. 3. -3. 9. + -4. -5. -6. -6. -4. -5. -6. -6. -2. -1. 0. -5. 0. 10. + -1. -3. -4. -3. -6. -3. -2. -5. -4. -5. -5. -2. -4. -6. 12. + 2. -2. 1. -1. -2. -1. -1. -1. -2. -4. -4. -1. -3. -4. -2. 7. + 0. -2. 0. -2. -2. -1. -2. -3. -3. -2. -3. -1. -1. -4. -3. 2. 8. + -5. -5. -7. -8. -5. -4. -6. -6. -4. -5. -4. -6. -3. 0. -7. -6. -5. 16. + -4. -4. -4. -6. -5. -3. -5. -6. 3. -3. -2. -4. -3. 4. -6. -3. -3. 3. 11. + -1. -4. -5. -6. -2. -4. -4. -6. -5. 4. 1. -4. 1. -2. -4. -3. 0. -5. -3. 7. +// -- 1.7.10.2