[Bioperl-l] help parsing msf file or clustalW file reports

[Jason Stajich]

I think you might want to use the column_from_residue_number method  
that is part of Bio::SimpleAlign - it lets you get the column from an  
alignment based on the sequence residue, doing some math along the way  
to deal with gaps. That is the residue -> alignment direction.  If you  
are starting at the alignment and want to get the residue's position  
you will use the location_from_column on a particular sequence so

     # select somehow a sequence from the alignment, e.g.
     my $seq = $aln->get_seq_by_pos(1);
     #$loc is undef or Bio::LocationI object
     my $loc = $seq->location_from_column(5);

-jason

On Sep 1, 2009, at 5:20 AM, Paola Bisignano wrote:

> Hi,
>
> I'm trying to parse fasta files, where I have couple of  
> alignments....I need to identify my residue in my alignment......I  
> have separate lists that derived from ligplot parsing files.. so I  
> have to manipulate string...but I don't now how to start..it seems  
> complicated..
> I used Bio::AlignIO to parse the fasta file, so I can have a parsed  
> file in msf or clustalW forma
>
> here an example:
> CLUSTAL W(1.81) multiple sequence alignment
>
>
> Sequence/9-273          
> DKWEMERTDITMKHKLGGGQYGEVYEGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAVMKE
> 2pl0:A/6-268           DEWEVPRETLKLVERLGAGQFGEVWMGYYNGHT- 
> KVAVKSLKQGSMSPDAFLAEANLMKQ
>                        *:**: *  :.: .:**.**:***:  
> * :: :: .****:**:.:*. : ** ** :**:
>
>
> Sequence/9-273          
> IKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYLRECNRQEVSAVVLLYMATQISSAME
> 2pl0:A/6-268           LQHQRLVRLYAVVTQEP- 
> IYIITEYMENGSLVDFLKTPSGIKLTINKLLDMAAQIAEGMA
>                        ::* .**:* .* *:** :*****:*   
> *.*:*:*:  .  :::   ** **:**:..*
>
> I  choose two residue for example...how can I extract  
> them...starting from their position in the pdb file?
> I need to walk...to my sequence
>
> I don't know if it is clear because I cannot explain the question  
> correctly in english...are there any Italians?
> could anyone help me?
>
>
>
>
>
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--
Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org