[EMBOSS] Searching for repeats in fuzznuc

[Steve Taylor]

Hi Peter,
> 
>> 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 :-)
> 

Excellent first suggestion!:-)

> 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

Thanks. That looks like a useful work around.

Out of interest any plans for a mismatch option in dreg?

Steve