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
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