[Bioperl-l] help parsing msf file or clustalW file reports
Paola Bisignano
paola_bisignano at yahoo.it
Tue Sep 1 12:20:25 UTC 2009
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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