[Bioperl-l] Parsing Clustalw alignment

Sendu Bala bix at sendu.me.uk
Mon Aug 7 15:40:25 EDT 2006

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:
and then get your answers from an AlignI:

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:

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

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