[EMBOSS] look for 'Ns' in a sequence using fuzznuc?

Fernan Aguero fernan.aguero at gmail.com
Fri Jun 14 17:09:06 UTC 2013


I guess I came across a problem ... I'm trying to rapidly find runs of Ns
in a nucleotide sequence, and produce the corresponding 'assembly_gap'
annotations in GFF format. This is all derived from scaffolded contigs.

I've tried fuzznuc first because it's easy to specify a pattern, and get a
list of locations in GFF format. However, fuzznuc uses N to mean any base.

Is there a way to subvert fuzznuc to use another character for this purpose?

Or maybe there's another emboss program to do this?

Thanks in advance for any pointer,


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