[EMBOSS] needle extended with reading frame information?

[Warren Gallin]

It might be more useful to you to align the protein sequences and then thread the corresponding nucleotide sequences onto that AA alignment “skeleton”

Translator X will do this for you automatically, given the ORFs, or you can provide a pre-run protein alignment if the alignment programs in TranslatorX are not suitable for you.

http://translatorx.co.uk/

You can either run on their server or, if your job is too big, download and install locally.

Warren Gallin

On Sep 30, 2014, at 2:27 PM, Adam Sjøgren <asjo at koldfront.dk> wrote:

>  Hi.
> 
> I want to align a DNA sequence where I know where the reading frame is,
> with another DNA sequence.
> 
> In the alignment I would prefer gaps to be opened/ended on codon
> boundaries (avoiding as much as I can what would be frameshifts).
> 
> I.e. in a simple example, I would prefer:
> 
>  GATGATTTTGA           GATGATTTTGA 
>  ||||||   ||    over   |||||   ||| 
>  GATGAT---GA           GATGA---TGA 
>  12312312312           12312312312   <-- reading frame pos
> 
> One way I guess the alignment could be nudged to give me results closer
> to what I want, is to have a gap open penalty which depends on the
> position in the reading frame.
> 
> Has anyone played around with this, or done something along these lines?
> 
>  Best regards,
> 
>    Adam
> 
> P.S. It seems that emboss.open-bio.org no longer accepts email?
> 
> -- 
> "Sadly, these days, if you know the difference               Adam Sjøgren
>  between a phillips- and a flat head screwdriver,       asjo at koldfront.dk
>  you're a renaissance man."
> 
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