[Bioperl-l] Bioperl clustalw Vs Online clustalw

[Anil Kumar]

Hi Forum  Members,

I have a doubt regarding Bioperl clustalw and it is as follows. If someone
know the solution, kindly suggest me.

Using Bioperl (clustalw 1.8V), I successfully aligned multiple sequences
from a .fasta file and saved it in clustalw format. However, the alignment
result is different from the  online clustalw result of the same sequences.

I guess that the change is due to some input parameters, but i failed to
provide the exact input parameter in order to get the alignment as online
clustalw.



Ani Lee
Seoul, ROK

Here is my code, (Also sending the input file (seq1.fasta), output file
(out.aln) and online output (online.aln.txt)

#!/usr/bin/perl
BEGIN { $ENV{CLUSTALDIR} = 'C:/clustalw'; }


use Bio::Tools::Run::Alignment::Clustalw;
use Bio::AlignIO;


$inputfilename = "seq1.fasta";
$in  = Bio::AlignIO->new(-file   => $inputfilename , ktuple => 2, matrix =>
BLOSUM, type => dna, extend => 0.1, gapopen => 10, gapext => 0.05,
                             format => 'fasta');



$out = Bio::AlignIO->new(-file   => ">out.aln" ,
                             -format => 'clustalw');



while ( my $aln = $in->next_aln() ) {
        $out->write_aln($aln);

                                   }
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CLUSTAL W (1.83) multiple sequence alignment


1               GTTGGTAATGAAGAAGACGAGACGACGACTTCCCCACTAGGAAACACGACGGAGGCGGAG
2               ------------------------------------------------------------
3               ------------------------------------------------------------
                                                                            

1               ATGATCGACGGCGGAGAGAGCTACAGAAACATCGATGCCTCCTGTCCAATCCCCCCATCC
2               ATGATCGACGGCGGAGAGAGCTACAGAAACATCGATGCCTCCTGTCCAATCCCCCCATCC
3               ------------------------------------------------------------
                                                                            

1               CATTCGGTAGTTGGATTGAAGACTACCGAATAAGAGAAGCAGGCAGGCAGACAAACCCTT
2               CATTCGGTAGTTGGATTGAAGACTACCGAATAAGAGAAGCAGGCAGGCAGACAAACCCTT
3               ------------------------------------------------------------
                                                                            

1               GAACCAAGGAGTCCTCGCTGAGGAAGCTTTGGATCCACGACGCAGCTATGGCCTCCCCGC
2               GAACCAAGGAGTCCTCGCTGAGGAAGCTTTGGATCCACGACGCAGCTATGGCCTCCCCGC
3               ------------------------------------------------------------
                                                                            

1               CCACCAGGCCGCCAGCCACAACCAGCTGACTAGGTAGGCTTCCTAGGTAGGGATCCCATC
2               CCACCAGGCCGCCAGCCACAACCAGCTGACTAGGTAGGCTTCCTAGGTAGGGATCCCATC
3               CCACCAGGCCGCCAGCCACAACCAGCTGACTAGGTAGGCTTCCTAGGTAGGGATCCCATC
                ************************************************************

1               CCTTCGATTCCCTACTCCCTCCCCCGATTGATTTGATTTGATTTGATTTAATTCGATTGC
2               CCTTCGATTCCCTACTCCCTCCCCCGATTGATTTGATTTGATTTGATTTAATTCGATTGC
3               CCTTCGATTCCCTACTCCCTCCCCCGATTGATTTGATTTGATTTGATTTAATTCGATTGC
                ************************************************************

1               CTGCTTTTCAGGTCGCATGCATCATCAGATTTCAATCTCCCTTCGTTCCCTGTCCCTAAT
2               CTGCTTTTCAGGTCGCATGCATCATCAGATTTCAATCTCCCTTCGTTCCCTGTCCCTAAT
3               CTGCTTTTCAGGTCGCATGCATCATCAGATTTCAATCTCCCTTCGTTCCCTGTCCCTAAT
                ************************************************************

1               CCAATACCAATAGGGAGCAATCAGCTGCTCCTCGACGGCGAGGGAGATGTCGTCGGCCGC
2               CCAATACCAATAGGGAGCAATCAGCTGCTCCTCGACGGCGAGGGAGATGTCGTCGGCCGC
3               CCAATACCAATAGGGAGCAATCAGCTGCTCCTCGACGGCGAGGGAGATGTCGTCGGCCGC
                ************************************************************

1               GGGCCAAGACAACGGAGATACCGCTGGGGACTACATCAAGTGGATGTGCGGCGCCGGTGG
2               GGGCCAAGACAACGGAGATACCGCTGGGGACTACATCAAGTGGATGTGCGGCGCCGGTGG
3               GGGCCAAGACAACGGAGATACCGCTGGGGACTACATCAAGTGGATGTGCGGCGCCGGTGG
                ************************************************************

1               CCGTGCGGGCGGCGCCATGGCCAACCTCCAGCGCGGCGTTGGCTCCCTCGTCCGTGACAT
2               CCGTGCGGGCGGCGCCATGGCCAACCTCCAGCGCGGCGTTGGCTCCCTCGTCCGTGACAT
3               CCGTGCGGGCGGCGCCATGGCCAACCTCCAGCGCGGCGTTGGCTCCCTCGTCCGTGACAT
                ************************************************************

1               TGGCGACCCCTGCCTCAACCCATCCCCCGTTAAGGTTCGCCTACTCCTACTCTAGCTCCA
2               TGGCGACCCCTGCCTCAACCCATCCCCCGTTAAGGTTCGCCTACTCCTACTCTAGCTCCA
3               TGGCGACCCCTGCCTCAACCCATCCCCCGTTAAGGTTCGCCTACTCCTACTCTAGCTCCA
                ************************************************************

1               TATGGATATGGATTCGATTAGCTGTCTACATTCTATGCCATCAATTTGTTTTCCATCACT
2               TATGGATATGGATTCGATTAGCTGTCTACATTCTATGCCATCAATTTGTTTTCCATCACT
3               TATGGATATGGATTCGATTAGCTGTCTACATTCTATGCCATCAATTTGTTTTCCATCACT
                ************************************************************

1               TCTCATTATACATCTCCATTGCTCTCTAAATTAAGGCTTCTCTAGCTCTATCCTATATAT
2               TCTCATTATACATCTCCATTGCTCTCTAAATTAAGGCTTCTCTAGCTCTATCCTATATAT
3               TCTCATTATACATCTCCATTGCTCTCTAAATTAAGGCTTCTCTAGCTCTATCCTATATAT
                ************************************************************

1               ATACTAGTACTCCGTATATGATTCTGCTTCATCACTTATTTATTCATCATCATACCGTGA
2               ATACTAGTACTCCGTATATGATTCTGCTTCATCACTTATTTATTCATCATCATACCGTGA
3               ATACTAGTACTCCGTATATGATTCTGCTTCATCACTTATTTATTCATCATCATACCGTGA
                ************************************************************

1               AGCTGTATAAGTCCTGTTATTTGTCATTTGGCATATGTTGTATAGATAACACTTTCAGCC
2               AGCTGTATAAGTCCTGTTATTTGTCATTTGGCATATGTTGTATAGATAACACTTTCAGCC
3               AGCTGTATAAGTCCTGTTATTTGTCATTTGGCATATGTTGTATAGATAACACTTTCAGCC
                ************************************************************

1               CAGGGACTTTCTATTGCCACTTTTATACATATACAATCAACATTTAGCATATGTATATCC
2               CAGGGACTTTCTATTGCCACTTTTATACATATACAATCAACATTTAGCATATGTATATCC
3               CAGGGACTTTCTATTGCCACTTTTATACATATACAATCAACATTTAGCATATGTATATCC
                ************************************************************

1               TGTACCGCTCAGTTGTACTGCTGCTTTGAAGATAATGTTTGCAAAACATATGAGCTCACA
2               TGTACCGCTCAGTTGTACTGCTGCTTTGAAGATAATGTTTGCAAAACATATGAGCTCACA
3               TGTACCGCTCAGTTGTACTGCTGCTTTGAAGATAATGTTTGCAAAACATATGAGCTCACA
                ************************************************************

1               CACGAGGCTAGATGCTGCATAGGCTGCACAATGGGGTAGCCATTTTGATACTTCTTAATG
2               CACGAGGCTAGATGCTGCATAGGCTGCACAATGGGGTAGCCATTTTGATACTTCTTAATG
3               CACGAGGCTAGATGCTGCATAGGCTGCACAATGGGGTAGCCATTTTGATACTTCTTAATG
                ************************************************************

1               CTATTTATGCTGGTCCAAATGTTCATTGGTAGCCTCAGGCAGAGAATTTTAGGGAGATAT
2               CTATTTATGCTGGTCCAAATGTTCATTGGTAGCCTCAGGCAGAGAATTTTAGGGAGATAT
3               CTATTTATGCTGGTCCAAATGTTCATTGGTAGCCTCAGGCAGAGAATTTTAGGGAGATAT
                ************************************************************

1               TATGTCAAACTCCCTGGATTCACTATGATTATACAATATTACCCATTCAATCCATTCAAA
2               TATGTCAAACTCCCTGGATTCACTATGATTATACAATATTACCCATTCAATCCATTCAAA
3               TATGTCAAACTCCCTGGATTCACTATGATTATACAATATTACCCATTCAATCCATTCAAA
                ************************************************************

1               TAAATTTCCAGGTCAACTCACATATTGTACTGAAAGAAGACTAATTTGCACTAATCATAT
2               TAAATTTCCAGGTCAACTCACATATTGTACTGAAAGAAGACTAATTTGCACTAATCATAT
3               TAAATTTCCAGGTCAACTCACATATTGTACTGAAAGAAGACTAATTTGCACTAATCATAT
                ************************************************************

1               CCTTTTATCCACCAGAGTATATGAGATTGTCTTCTATATGCAATTTACTTCATATCGACA
2               CCTTTTATCCACCAGAGTATATGAGATTGTCTTCTATATGCAATTTACTTCATATCGACA
3               CCTTTTATCCACCAGAGTATATGAGATTGTCTTCTATATGCAATTTACTTCATATCGACA
                ************************************************************

1               TTTTTCTGCAGAATTGCAAAACTGACGCCTTGTTTTCCATCTGGAATTGTGCAGGGGAGC
2               TTTTTCTGCAGAATTGCAAAACTGACGCCTTGTTTTCCATCTGGAATTGTGCAGGGGAGC
3               TTTTTCTGCAGAATTGCAAAACTGACGCCTTGTTTTCCATCTGGAATTGTGCAGGGGAGC
                ************************************************************

1               AAAATGCTCAAACCGGAAAAATGGCACACATGTTTTGATAATGATGGAAAGGTCATAGGT
2               AAAATGCTCAAACCGGAAAAATGGCACACATGTTTTGATAATGATGGAAAGGTCATAGGT
3               AAAATGCTCAAACCGGAAAAATGGCACACATGTTTTGATAATGATGGAAAGGTCATAGGT
                ************************************************************

1               TTCCGTAAAGCCCTAAAATTCATTGTCTTAGGGGTGAGTTAATTGTTTCTTTTGTGCTTC
2               TTCCGTAAAGCCCTAAAATTCATTGTCTTAGGGGTGAGTTAATTGTTTCTTTTGTGCTTC
3               TTCCGTAAAGCCCTAAAATTCATTGTCTTAGGGGTGAGTTAATTGTTTCTTTTGTGCTTC
                ************************************************************

1               AAAAACTTGTTTTTTCATGTATTTTAGCTGTTGAAGGGTGTGGATTTTTTTTTCAGTCTT
2               AAAAACTTGTTTTTTCATGTATTTTAGCTGTTGAAGGGTGTGGATTTTTTTTTCAGTCTT
3               AAAAACTTGTTTTTTCATGTATTTTAGCTGTTGAAGGGTGTGGATTTTTTTTTCAGTCTT
                ************************************************************

1               AATACATTACCTTTTAGAGCATGATGCCCCACGCGCCATTTGTGAATGTGTAAAATAGGG
2               AATACATTACCTTTTAGAGCATGATGCCCCACGCGCCATTTGTGAATGTGTAAAATAGGG
3               AATACATTACCTTTTAGAGCATGATGCCCCACGCGCCATTTGTGAATGTGTAAAATAGGG
                ************************************************************

1               AAGATCAAATAGAACGTGACAACTGTTTATTTTATTACCATGATCATTGTTCTCTTTGAG
2               AAGATCAAATAGAACGTGACAACTGTTTATTTTATTACCATGATCATTGTTCTCTTTGAG
3               AAGATCAAATAGAACGTGACAACTGTTTATTTTATTACCATGATCATTGTTCTCTTTGAG
                ************************************************************

1               AGTGTCTGCTTTGGAAATTTCAAAGAAATTAATGCATATGATTGCGTAGCTCTAGTTTTT
2               AGTGTCTGCTTTGGAAATTTCAAAGAAATTAATGCATATGATTGCGTAGCTCTAGTTTTT
3               AGTGTCTGCTTTGGAAATTTCAAAGAAATTAATGCATATGATTGCGTAGCTCTAGTTTTT
                ************************************************************

1               CTTAAAAAAATAAGCGGCTAGGCTCTTTATACTATTATGTCACAGAGTGTTTGCCTTTTA
2               CTTAAAAAAATAAGCGGCTAGGCTCTTTATACTATTATGTCACAGAGTGTTTGCCTTTTA
3               CTTAAAAAAATAAGCGGCTAGGCTCTTTATACTATTATGTCACAGAGTGTTTGCCTTTTA
                ************************************************************

1               CCTGTGTATGTAGCTAGGCATAAACATTTGTTTGTGGGTAAATACAAAAAAAAATCCAAT
2               CCTGTGTATGTAGCTAGGCATAAACATTTGTTTGTGGGTAAATACAAAAAAAAATCCAAT
3               CCTGTGTATGTAGCTAGGCATAAACATTTGTTTGTGGGTAAATACAAAAAAAAATCCAAT
                ************************************************************

1               GTGTAGAAACTGCTTATAAATACATAAAAGTTACATAAATACATAACTGCTTCAAATAAG
2               GTGTAGAAACTGCTTATAAATACATAAAAGTTACATAAATACATAACTGCTTCAAATAAG
3               GTGTAGAAACTGCTTATAAATACATAAAAGTTACATAAATACATAACTGCTTCAAATAAG
                ************************************************************

1               CAAGATTTGAACATACCTTCACATAAGCTTTCCCCTAACTGAAAAGCCATTTGGTATAAC
2               CAAGATTTGAACATACCTTCACATAAGCTTTCCCCTAACTGAAAAGCCATTTGGTATAAC
3               CAAGATTTGAACATACCTTCACATAAGCTTTCCCCTAACTGAAAAGCCATTTGGTATAAC
                ************************************************************

1               CTTATAGAAATTAGATATAGTGGAGATGTGGAATGAGCTGCTATCAAGTCTTGTTTCGTG
2               CTTATAGAAATTAGATATAGTGGAGATGTGGAATGAGCTGCTATCAAGTCTTGTTTCGTG
3               CTTATAGAAATTAGATATAGTGGAGATGTGGAATGAGCTGCTATCAAGTCTTGTTTCGTG
                ************************************************************

1               AAAGCAAACTGACACGGTCTCCACAGCAAACACGTCCACAGCTTTGCAATTAGTATCTTT
2               AAAGCAAACTGACACGGTCTCCACAGCAAACACGTCCACAGCTTTGCAATTAGTATCTTT
3               AAAGCAAACTGACACGGTCTCCACAGCAAACACGTCCACAGCTTTGCAATTAGTATCTTT
                ************************************************************

1               ATAGGAAGGTCAATCAGAGTTCATTGGCCATATCTTGGAAAAAAAAGGCATCAGATTTTA
2               ATAGGAAGGTCAATCAGAGTTCATTGGCCATATCTTGGAAAAAAAAGGCATCAGATTTTA
3               ATAGGAAGGTCAATCAGAGTTCATTGGCCATATCTTGGAAAAAAAAGGCATCAGATTTTA
                ************************************************************

1               GTTTAATTATGTCTATATTTTAGGCATGGATTATTGATCATTTTTGCAGCAGACTAAGTT
2               GTTTAATTATGTCTATATTTTAGGCATGGATTATTGATCATTTTTGCAGCAGACTAAGTT
3               GTTTAATTATGTCTATATTTTAGGCATGGATTATTGATCATTTTTGCAGCAGACTAAGTT
                ************************************************************

1               TAATGCATGTAGTTATTTTCCTTGATTAGTGATTAGTGTTGTTATTTTCTATACACCACT
2               TAATGCATGTAGTTATTTTCCTTGATTAGTGATTAGTGTTGTTATTTTCTATACACCACT
3               TAATGCATGTAGTTATTTTCCTTGATTAGTGATTAGTGTTGTTATTTTCTATACACCACT
                ************************************************************

1               GGCACTGATAGATGTGCTCCATGCTTTGCAATGCATCAAAATTATCATATCGTGCCTAAC
2               GGCACTGATAGATGTGCTCCATGCTTTGCAATGCATCAAAATTATCATATCGTGCCTAAC
3               GGCACTGATAGATGTGCTCCATGCTTTGCAATGCATCAAAATTATCATATCGTGCCTAAC
                ************************************************************
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