[Bioperl-l] help correcting reading frames

[yang liu]

Dear colleagues,

I have a bunch protein-coding gene sequences need to clean, as some of them
are in bad qualities, with insertions or deletions that breaking the
reading frame here and there. I am wondering is there a way to correct the
reading frames by deleting the whole codon if a mutation happens in that
codon using Perl. For example, make

> Taxon

ATG TTT GTT A-T GCG GGC GGT

to:

>Taxon

ATG TTT GTT ---  GCG GGC GGT

I have many genes like this.

Any help is appreciated,

Thanks.