[Bioperl-l] Parsing Clustalw alignment

[Sendu Bala]

Amanda n/a wrote:
> Hi,
> Has anyone had luck in using Clustalw.pm to parse through clustalw .aln
> and/or output files? Specifically, I'm looking to search for high scoring
> alignments between specific pairs of sequences. If found, I then need to
> extract the two sequence ids, sequences, alignment score and positions.

You'll want to use the Bio::AlignIO module for clustalw.

You read your file with AlignIO:
http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/AlignIO.html
and then get your answers from an AlignI:
http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Align/AlignI.html

That's perhaps not the easiest thing to get to grips with, but the 
AlignIO modules are kind of similar in concept to the SeqIO ones, for 
which there is a more friendly explanation:
http://www.bioperl.org/wiki/HOWTO:SeqIO

Also, http://www.bioperl.org/wiki/HOWTO:Beginners.