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

[Andres Pinzon]

Hi,
Im trying fuzznuc to search for some patterns in a a genome.
When I search the forward strand:
fuzznuc -sequence mysqeq.gb -pattern 'TTC[GTC]-N(14,17)-TTC[GAT]'
-outfile myseq.fuzznuc -rformat2 genbank

Everything is ok.


...But when I search the complementary strand:
fuzznuc -sequence mysqeq.gb -pattern 'TTC[GTC]-N(14,17)-TTC[GAT]'
-outfile myseq-rev.fuzznuc -rformat2 genbank -complement

It appears to do it well, I mean that it searches for the pattern on
both strands, but when I take a closer look to the output file, this
is what I got:
===================
misc_feature    676..700
                     /note="*pat pattern1"
misc_feature    12325..12349
                     /note="*pat pattern1"
.
.
.
.

misc_feature    complement(676..700)
                     /note="*pat pattern1"
misc_feature    complement(12325..12349)
                     /note="*pat pattern1"
======================

It reports a pattern on complement  that exists, in fact, but on the
forward strand not in complement.

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

Regards,
-- 
Andrés Pinzón cPh.D.
http://groups.google.com/group/Bioinformatica_es
Bioinformatics Center, Colombia EMBnet node
http://bioinf.ibun.unal.edu.co
Tel +57 3165000 ext 16961 Fax +571 3165415
Micology and Phytopathology Laboratory - Los Andes University.
Tel +571 3394949 ext. 2768