[EMBOSS] needle extended with reading frame information?

[Adam Sjøgren]

  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."