[EMBOSS] stretches of nucleotides/aa

[Stefanie Lager]

It's a problem that there isn't an EMBOSS program that fully can
replace the GCG program FindPatterns. FindPatterns can use a database
of patterns to search sequences. It's possible to use the EMBOSS
program tfscan, and to make your own database in the same format as
tfscan uses. I ended up using the program TACG
(http://tacg.sourceforge.net/)  since that both can use a database of
patterns and report hits in both strands of the sequence (option -S2).

Stefanie


 
> 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.
> 
> 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

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