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