[EMBOSS] fuzznuc

[uludag at ebi.ac.uk]

> I am using EMBOSS 6.1.0 and I wonder why the '-mismatch' qualifier of
> fuzznuc is missing in the new EMBOSS version.

In latest EMBOSS releases the '-mismatch' option seems to be renamed as
'-pmismatch' as it became one of the associated qualifiers of '-pattern'
option.

http://emboss.open-bio.org/wiki/Appdoc:Fuzznuc#Command_line_arguments

> Is there an alternative for fuzznuc for searching short DNA motifs?

Do you search your DNA motifs in one/few long sequence(s) or in several
short sequences?

Regards,
Mahmut