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
