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- From: "olivier.rue" <Olivier.Rue@toulouse.inra.fr>
- To: fasta_list@virginia.edu
- Subject: ssearch36 different results with same command
- Date: Fri, 30 Aug 2013 10:16:25 +0200
Hello Mr Pearson,
I use ssearch36 and I am quite surprised to get different outputs when I run the same command line multiple times. Here are the two outputs : # /home/olivier/Installations/fasta-36.3.6/bin/ssearch36 -E 7 -m 1 -3 -f -1 -g -1 -w 200 -s hybridation_matrix.mat potential_mir_scaffold_10328_5401_5419_0.fa before_scaffold_10328_5401_5419_0.fa SSEARCH performs a Smith-Waterman search version 36.3.6 June, 2013(preload9) Please cite: T. F. Smith and M. S. Waterman, (1981) J. Mol. Biol. 147:195-197; W.R. Pearson (1991) Genomics 11:635-650 Parameters not available for: hybridation_matrix.mat: -1/-1 Query: potential_mir_scaffold_10328_5401_5419_0.fa 1>>>scaffold_10328_5401_5419_0 - 19 nt (forward-only) Library: before_scaffold_10328_5401_5419_0.fa 200 residues in 1 sequences Statistics: (shuffled [500]) MLE statistics: Lambda= 0.6170; K= 17.62 statistics sampled from 1 (1) to 500 sequences Algorithm: Smith-Waterman (PGopt) (7.2 Nov 2010) Parameters: hybridation_matrix.mat matrix (2:-1), open/ext: -1/-1 Scan time: 0.020 The best scores are: &nb sp; s-w bits E(1) before & nbsp; ( 200) [f] 19 12.8 0.42 >>before ; (200 nt) s-w opt: 19 Z-score: 50.3 bits: 12.8 E(1): 0.42 Smith-Waterman score: 19; 0.0% identity (91.7% similar) in 12 nt overlap (7-18:137-148) 10 scaff CGGTGGGAAACGGAACTAC xxxxxXxxxxxx before CACCTAATACCTTTTTTGCACAATTGGTTAGAGCCTGTAAGTAAGCATTTCACTGTAAGGTCTACTACACATGTTGTTTTCGGCGCACGTGACATATAAACTTTGATTTGATTTGATAATCTCATGAAGCTGGTTGAGAGAATGCCAATAGTTTGCAAAGCTGT 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 19 residues in 1 query sequences 200 residues in 1 library sequences Tcomplib [36.3.6 June, 2013(preload9)] (2 proc in memory [0G]) start: Fri Aug 30 08:56:20 2013 done: Fri Aug 30 08:56:20 2013 Total Scan time: 0.020 Total Display time: 0.000 Function used was SSEARCH [36.3.6 June, 2013(preload9)] and # /home/olivier/Installations/fasta-36.3.6/bin/ssearch36 -E 7 -m 1 -3 -f -1 -g -1 -w 200 -s hybridation_matrix.mat potential_mir_scaffold_10328_5401_5419_0.fa before_scaffold_10328_5401_5419_0.fa SSEARCH performs a Smith-Waterman search version 36.3.6 June, 2013(preload9) Please cite: T. F. Smith and M. S. Waterman, (1981) J. Mol. Biol. 147:195-197; W.R. Pearson (1991) Genomics 11:635-650 Parameters not available for: hybridation_matrix.mat: -1/-1 Query: potential_mir_scaffold_10328_5401_5419_0.fa 1>>>scaffold_10328_5401_5419_0 - 19 nt (forward-only) Library: before_scaffold_10328_5401_5419_0.fa 200 residues in 1 sequences Statistics: (shuffled [500]) MLE statistics: Lambda= 0.5685; K= 6.637 statistics sampled from 1 (1) to 500 sequences Algorithm: Smith-Waterman (PGopt) (7.2 Nov 2010) Parameters: hybridation_matrix.mat matrix (2:-1), open/ext: -1/-1 Scan time: 0.020 The best scores are: &nb sp; s-w bits E(1) before & nbsp; ( 200) [f] 19 12.9 0.4 >>before ; (200 nt) s-w opt: 19 Z-score: 50.7 bits: 12.9 E(1): 0.4 Smith-Waterman score: 19; 0.0% identity (91.7% similar) in 12 nt overlap (7-18:137-148) 10 scaff CGGTGGGAAACGGAACTAC xxxxxXxxxxxx before CACCTAATACCTTTTTTGCACAATTGGTTAGAGCCTGTAAGTAAGCATTTCACTGTAAGGTCTACTACACATGTTGTTTTCGGCGCACGTGACATATAAACTTTGATTTGATTTGATAATCTCATGAAGCTGGTTGAGAGAATGCCAATAGTTTGCAAAGCTGT 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 >-- s-w opt: 18 Z-score: 46.3 bits: 12.0 E(1): 0.6 Smith-Waterman score: 18; 0.0% identity (75.0% similar) in 20 nt overlap (4-18:45-64) 10 @ scaff CGGTGGGAAA--CG-G--AACTAC xxxxxxx xx x xxxxx before TTTACTGTTGTTTTATTTCTTTACTTACCTATGGTTCACCTAATACCTTTTTTGCACAATTGGTTAGAGCCTGTAAGTAAGCATTTCACTGTAAGGTCTACTACACATGTTGTTTTCGGCGCACGTGACATATAAACTTTGATTTGATTTGATAATCTCATGAAGCTGGTTGAGAGAATGCCAATAGTTTGCAAAGCTGT 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 19 residues in 1 query sequences 200 residues in 1 library sequences Tcomplib [36.3.6 June, 2013(preload9)] (2 proc in memory [0G]) start: Fri Aug 30 08:57:09 2013 done: Fri Aug 30 08:57:09 2013 Total Scan time: 0.020 Total Display time: 0.000 Function used was SSEARCH [36.3.6 June, 2013(preload9)] I attach the files if you want to run the commands by yourself. I tried with the last updated version, but results are the same. Do you have any explanation ? Thanks for advance, -- ======================================================== Olivier RUÉ INRA - MIAT - Plateforme Bioinfo-Genotoul Chemin de Borde-Rouge - Auzeville - CS 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33 (0)5.61.28.54.93 http://www.bioinfo.genotoul.fr/ |
TTTACTGTTGTTTTATTTCTTTACTTACCTATGGTTCACCTAATACCTTTTTTGCACAATTGGTTAGAGCCTGTAAGTAAGCATTTCACTGTAAGGTCTACTACACATGTTGTTTTCGGCGCACGTGACATATAAACTTTGATTTGATTTGATAATCTCATGAAGCTGGTTGAGAGAATGCCAATAGTTTGCAAAGCTGT# RNA matrix favorising hybridation
A C G T U R Y M W S K D H V B N X
A -1 -1 -1 2 2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
C -1 -1 2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
G -1 2 -1 0 0 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
T 2 -1 0 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
U 2 -1 0 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
R -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
Y -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
M -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
W -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
S -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
K -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
D -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
H -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
V -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
B -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
N -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1>scaffold_10328_5401_5419_0
CGGTGGGAAACGGAACTAC
- ssearch36 different results with same command, olivier.rue, 08/30/2013
- Re: ssearch36 different results with same command, William Pearson, 08/30/2013
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