[Bioperl-l] help correcting reading frames

yang liu yang.liu0508 at gmail.com
Sat Mar 15 23:32:51 UTC 2014


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.



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