[Biopython-dev] Weekly Update for Codon Alignment GSoC project

[Eric Talevich]

On Sun, Jul 21, 2013 at 7:55 PM, Zheng Ruan <zruan1991 at gmail.com> wrote:

> Hi,
>
> I post an update for the project last week in my blog<http://zruanweb.com/> as
> well as my plan next week. As the midterm evaluation deadline is
> approaching, I also include this into it. Thanks for your comments and
> suggestions.
>
> Best,
> Zheng Ruan
>

Hey Zheng,

Great progress so far. Your implementation of codon alignment up to this
point looks more than adequate to me. A couple thoughts:

- Can your implementation detect inserts (forward frameshifts) of more than
3 nucleotides, as might be introduced by introns? Or just 1-2 bases?

- Same question for the backward frameshift implementation. One biological
cause for these backward shifts is ribosomal slippage -- these are usually
short, e.g. 1 base, so it is not urgent for your implementation to handle
larger backward shifts if this would be more difficult. (For drastic
differences between protein and nucleotide sequences, a bioinformatician
would normally use some variant of BLAST, exonerate, or another local
alignment tool, rather than expecting this codon alignment algorithm to
catch and handle every possibility.)

Have a safe trip home!

-Eric