[EMBOSS] needle extended with reading frame information?
Warren Gallin
wgallin at ualberta.ca
Tue Sep 30 20:51:02 UTC 2014
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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