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ssearch36 different results with same command


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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/ 


>before
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


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