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

[Paola Bisignano]

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?