[EMBOSS] Searching for repeats in fuzznuc

[Peter Rice]

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