[EMBOSS] dreg: does it search both strands?

[david.bauer at bayer.com]

Hi Daniel & Peter,

emboss-bounces at lists.open-bio.org schrieb am 12/02/2011 17:58:32:

> 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.
> 

I think another candidate would be fuzznuc. 
(That's at least the program, where I sometimes missed this option ;-)

> Interesting suggestion.
> 
> Maybe we can add a -bothstrands option for applications to search the 
> forward and reverse strands.

Yes, this would add the new functionality without breaking the old default 
behaviour of the programs.

> We need to consider:
> * Do the results make sense?
> * What default do we set (maybe some programs have a different default)?

As mentioned above, I would not touch the old default settings and add 
searching both strands as an option.
(e.g. in stssearch the search of both strands is already the default.)

> * Is this complicated for programs that can use DNA or protein input?
> * Can we apply it to applications aligning two sequences?

I think it could make sense for programs which can align one sequence 
against a set of
other sequences (e.g. water, needle). 

Regards,
David.