[EMBOSS] stretches of nucleotides/aa

Henrikki Almusa henrikki.almusa at helsinki.fi
Mon Jan 19 07:20:53 UTC 2004

On Sunday 18 January 2004 19:44, peter robinson wrote:
> Hi all,
> I am interested in looking for all strecthes of any of the nucleotides
> longer that a certain minimum (say 10) in a sequence and having the program
> report back all hits including actual length and location within the
> sequence.

If i read that correctly, then dreg can do this. Pattern that should do this 
is "T{10}|A{10}|C{10}|G{10}" (dreg and preg will transform the sequence and 
pattern into uppercase so no need to use "[tT]"). Dreg and preg pages in 
emboss website are quite helpful for further use the programs (got upgraded 
in 2.8.0). 

> While there are several EMBOSS programs that could be set up to do
> something like this for each nucleotide at a time (eg fuzznuc), I was
> wondering if there is any program that could do this for all characters at
> once, or failing that, if anyone has any suggestions as to which EMBOSS
> program might be a suitable candidate for modification to this purpose?
> Thanks
> Peter

Here to help,
Henrikki Almusa

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