[EMBOSS] Fuzznuc question: how to search complementary strand?
pmr at ebi.ac.uk
Mon Feb 26 11:24:59 EST 2007
Andres Pinzon wrote:
> 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,
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