[EMBOSS] needle extended with reading frame information?

[Daniel Barker]

Additionally: I wonder if homology-based primary genome annotation software may be relevant? E.g. Genewise (Wise2 package) tries to find a plausible gene structure AND a decent level of sequence similarity.

http://www.ebi.ac.uk/Tools/psa/genewise/help

I know Exonerate less well, but I expect it can do similar things and more (likely more rapidly):

https://www.ebi.ac.uk/~guy/exonerate/

Presumably these packages have settings about whether introns are expected or not (eukaryotic genomic DNA vs transcript sequence), specific penalties, etc.

There are other tools for prokaryotes, I think.

- Daniel

Daniel Barker
http://biology.st-andrews.ac.uk/staff/db60
The University of St Andrews is a charity registered in Scotland :
No SC013532

________________________________________
From: emboss-bounces+db60=st-andrews.ac.uk at mailman.open-bio.org [emboss-bounces+db60=st-andrews.ac.uk at mailman.open-bio.org] on behalf of David Bauer [david.bauer at bayer.com]
Sent: 01 October 2014 06:47
To: Warren Gallin; emboss at mailman.open-bio.org
Subject: Re: [EMBOSS] needle extended with reading frame information?

Hi,

did you try the EMBOSS tranalign ?

tranalign       Generate an alignment of nucleic coding regions from aligned proteins

Kind regards,
David.

-----Ursprüngliche Nachricht-----
Von: emboss-bounces+david.bauer=bayer.com at mailman.open-bio.org [mailto:emboss-bounces+david.bauer=bayer.com at mailman.open-bio.org] Im Auftrag von Warren Gallin
Gesendet: 30 September 2014 22:51
An: emboss at mailman.open-bio.org
Betreff: Re: [EMBOSS] needle extended with reading frame information?

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."
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/emboss


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