[Bioperl-l] Translate sequences align and reverse translate

Albert Vilella avilella at gmail.com
Thu Jan 18 10:53:00 EST 2007


There are some dirty dirty scripts in:

http://ortholytics.googlecode.com/svn/create_alignment_sets.PLS
(this one relies on orthology info from orthomcl)

http://ortholytics.googlecode.com/svn/launch_probcons_sets.PLS
http://ortholytics.googlecode.com/svn/launch_aa_to_cds_dna.PLS

You may find some of the stuff of interest,

Cheers,

    Albert.

On 1/18/07, Anthony Underwood <Anthony.Underwood at hpa.org.uk> wrote:
> Hi All,
>
>
>
> I would like to automate the process of taking coding DNA sequences,
> translating them to amino acids, aligning them with clustalw and then
> reverse-translating back to DNA so as to obtain the best alignment. I
> can think of how I would do this with bioperl but since it is probably a
> common process  I would like to ask if anyone already has such a script
> that they wouldn't mind sharing so I don't re-invent the wheel.
>
>
>
> Many thanks,
>
>
>
> Anthony
>
>
>
>
> -----------------------------------------
> *******************************************************************
> *******
> The information contained in the EMail and any attachments is
> confidential and intended solely and for the attention and use of
> the named addressee(s). It may not be disclosed to any other person
> without the express authority of the HPA, or the intended
> recipient, or both. If you are not the intended recipient, you must
> not disclose, copy, distribute or retain this message or any part
> of it. This footnote also confirms that this EMail has been swept
> for computer viruses, but please re-sweep any attachments before
> opening or saving. HTTP://www.HPA.org.uk **************************
> ************************************************
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


More information about the Bioperl-l mailing list