Thread nucleotides onto a protein alignment (back-translation)

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Thread nucleotides onto a protein alignment (back-translation)

Peter Cock
Hi all,

If anyone is interested, I've just wrapped a little Python script
I'd prepared early for use in Galaxy for a fairly common need -
"back translating" a protein alignment into a nucleotide alignment
by threading the unaligned sequence.

We're testing this locally, and barring any major issues I
would expect to release this to the main Tool Shed in a week
or so - but if any of you want to have a play with it now, and
pass on feedback, please do so:

Development repository:
https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans

Test Tool Shed release:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/align_back_trans

Planned Tool Shed release:
http://toolshed.g2.bx.psu.edu/view/peterjc/align_back_trans (pending)

This uses Biopython's AlignIO [*] module and so can handle a
range of alignment file formats - for now I have restricted this
to "fasta", "clustal" and "phylip" which I believe are all already
in use on the tool shed - there is probably scope here for a
more coordinated effort to define Galaxy datatypes in this
area, including things like the PFAM/Stockholm format and
strict/relaxed variants of PHYLIP.

Regards,

Peter

[*] http://biopython.org/wiki/AlignIO
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Re: Thread nucleotides onto a protein alignment (back-translation)

Peter Cock
This new tool is now live on the main Tool Shed:
http://toolshed.g2.bx.psu.edu/view/peterjc/align_back_trans

Peter

On Tue, Feb 18, 2014 at 2:10 PM, Peter Cock <[hidden email]> wrote:

> Hi all,
>
> If anyone is interested, I've just wrapped a little Python script
> I'd prepared early for use in Galaxy for a fairly common need -
> "back translating" a protein alignment into a nucleotide alignment
> by threading the unaligned sequence.
>
> We're testing this locally, and barring any major issues I
> would expect to release this to the main Tool Shed in a week
> or so - but if any of you want to have a play with it now, and
> pass on feedback, please do so:
>
> Development repository:
> https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans
>
> Test Tool Shed release:
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/align_back_trans
>
> Planned Tool Shed release:
> http://toolshed.g2.bx.psu.edu/view/peterjc/align_back_trans (pending)
>
> This uses Biopython's AlignIO [*] module and so can handle a
> range of alignment file formats - for now I have restricted this
> to "fasta", "clustal" and "phylip" which I believe are all already
> in use on the tool shed - there is probably scope here for a
> more coordinated effort to define Galaxy datatypes in this
> area, including things like the PFAM/Stockholm format and
> strict/relaxed variants of PHYLIP.
>
> Regards,
>
> Peter
>
> [*] http://biopython.org/wiki/AlignIO
___________________________________________________________
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