[Bioperl-l] help correcting reading frames

[Jing Yu]

On 15 Mar 2014, at 23:32, yang liu <yang.liu0508 at gmail.com> wrote:

> 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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Are all mutations, deletions and insertions represented by a hyphen?

J