[Bioperl-l] Selecting columns from alignment

Felix Schlesinger schlesi at ebi.ac.uk
Wed Jun 27 07:57:27 EDT 2007


is there an elegant way to select columns from an alignment object
fulfilling a certain property (for example less than x gaps)?
Everything I can see from Align::AlignI seems to involve looking at
the individual sequences, creating lots of slices and appending them.
If there a better way in bioperl or failing that, does anyone know a
software package with similar functionality (t-coffee has lots of
filters for alignments, but nothing to select columns besides by
position it seems). Ideally this would also return a mapping from old
to new positions in one of the sequences of course.


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