[EMBOSS] Fuzznuc question: how to search complementary strand?

[Peter Rice]

Andres Pinzon wrote:
> Hi,
> Im trying fuzznuc to search for some patterns in a a genome.
> 
> ...But when I search the complementary strand:
>
> It reports a pattern on complement  that exists, in fact, but on the
> forward strand not in complement.
> 
> Am I doing something wrong?

I think this is one we patched soon after the 4.0.0 release. There are patches 
on our FTP server, and a new 4.1.0 release will appear soon with this fix included.

> What options do I have to use in order to make fuzznuc to report the
> occurrences of  "pattern" on both: reverse and complementary strand?

-complement is correct. It searched both strands.

To search only the complementary strand, use the general EMBOSS option -sreverse 
and do not specify -complement

Hope this helps,

Peter