[EMBOSS] dreg: does it search both strands?

[Peter Rice]

Dear Daniel,

On 12/02/2011 12:07, Daniel Barker wrote:
> A lot of the time for nucleotide stuff it makes sense to search both
> strands. Of course, it isn't hard to search one strand, then the other.
> But this introduces an extra step. I wonder if there could be some
> convenient option to do this, and if it should perhaps be the default?
> (As with NCBI blastall with any kind of nucleotide search.)
>
> This would affect programs beyond just dreg and, though it would be OK
> for our work, perhaps it wouldn't make sense for others. Just a thought.

Interesting suggestion.

Maybe we can add a -bothstrands option for applications to search the 
forward and reverse strands. We need to consider:

* Do the results make sense?
* What default do we set (maybe some programs have a different default)?
* Is this complicated for programs that can use DNA or protein input?
* Can we apply it to applications aligning two sequences?

meanwhile, running twice with -sreverse the second time will find you 
all the matches.

regards,

Peter Rice
EMBOSS Team