[EMBOSS] Searching for repeats in fuzznuc
Peter Rice
pmr at ebi.ac.uk
Thu Jun 21 16:31:54 UTC 2007
Hi Steve,
> I would like to search for a specific repeat using fuzznuc. It is pretty easy using a regexp in preg (yes, I know preg should really only be used for protein sequences:-)) via
>
> preg -pattern '(TG{5,20}){2,10}'
>
> but is there a way to do something similar in fuzznuc, since I would like to introduce mismatches.
You could use dreg rather than preg :-)
Fuzznuc now accepts files with a pattern on each line:
% cat tg.pat
TG(5,20)TG(5,20)
TG(5,20)TG(5,20)TG(5,20)
TG(5,20)TG(5,20)TG(5,20)TG(5,20)
TG(5,20)TG(5,20)TG(5,20)TG(5,20)TG(5,20)
or, if you want to name them, ...
% cat tg.pat
>tg2
TG(5,20)TG(5,20)
>tg3
TG(5,20)TG(5,20)TG(5,20)
>tg4
TG(5,20)TG(5,20)TG(5,20)TG(5,20)
>tg5
TG(5,20)TG(5,20)TG(5,20)TG(5,20)TG(5,20)
You can use the file with:
% fuzznuc -pattern @tg.pat
Hope that helps,
Peter
More information about the EMBOSS
mailing list