[Bioperl-l] problems with clustalw

vdar at yorku.ca vdar at yorku.ca
Mon May 12 14:19:27 EDT 2008


Thanks a lot! You have solved the problem. I am getting the following output
now. Would it be possible for you to let me know how can I print the
alignments? I need the alignments as we get after running web-based clustalw or
multalin programs.



CLUSTAL W (1.83) Multiple Sequence Alignments



Sequence format is Pearson
Sequence 1: thal             77 bp
Sequence 2: lyrata           77 bp
Sequence 3: boechera         77 bp
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score:  100
Sequences (1:3) Aligned. Score:  100
Sequences (2:3) Aligned. Score:  100
Guide tree        file created:   [/tmp/EIZp1pI1gi/jKZ8gRG2dY.dnd]
Start of Multiple Alignment
There are 2 groups
Aligning...
Group 1: Sequences:   2      Score:1463
Group 2: Sequences:   3      Score:1463
Alignment Score 1551
GCG-Alignment file created      [/tmp/EIZp1pI1gi/Wa9Du2UIum]

Nisa



Quoting Sendu Bala <bix at sendu.me.uk>:

> vdar at yorku.ca wrote:
> > Yes, seems like it worked, now I am having the following error message
> which is
> > not because of the errors in installation..right?
> >
> > $ perl mult_align.pl
> > Can't call method "isa" without a package or object reference at
> > /opt/rocks/lib/perl5/site_perl/5.8.8//Bio/Tools/Run/Alignment/Clustalw.pm
> line
> > 617.
>
> You weren't passing sequence objects to align() due to another error in
> your script:
>
> Instead of:
> my @seq_array = qw/$seq_obj_on $seq_obj_too $seq_obj_thre/;
> my $seq_array_ref = \@seq_array;
> my $aln = $factory->align($seq_array_ref);
>
> You can have:
> my @seq_array = ($seq_obj_on, $seq_obj_too, $seq_obj_thre);
> my $seq_array_ref = \@seq_array;
> my $aln = $factory->align($seq_array_ref);
>
> Or just:
> my $aln = $factory->align([$seq_obj_on, $seq_obj_too, $seq_obj_thre]);
>




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