Hi, did you try the EMBOSS tranalign ?
tranalign Generate an alignment of nucleic coding regions from aligned proteins Kind regards, David. -----Ursprüngliche Nachricht----- Von: [email protected] [mailto:[email protected]] Im Auftrag von Warren Gallin Gesendet: 30 September 2014 22:51 An: [email protected] 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 <[email protected]> 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, [email protected] > you're a renaissance man." > > _______________________________________________ > EMBOSS mailing list > [email protected] > http://mailman.open-bio.org/mailman/listinfo/emboss _______________________________________________ EMBOSS mailing list [email protected] http://mailman.open-bio.org/mailman/listinfo/emboss _______________________________________________ EMBOSS mailing list [email protected] http://mailman.open-bio.org/mailman/listinfo/emboss
