[BiO BB] finding repeat sequences

[J.W. Bizzaro]

There is a nascent article on the topic here (mostly about nomenclature right now):

  http://wiki.bioinformatics.org/Repetitive_DNA_sequence

If anyone would like to contribute to it, please do.

There are a number of programs available for finding repetitive sequences.  Since you're looking for tandem repeats, that narrows it down some.  There are differences in scale as well: are you looking for short or long repeating units?

The methods for finding repeats vary, too.  Some use a library of known repeats (good for larger repeating units), while others take a de novo, "all possible combinations" approach.

And gaps are an important consideration.  Some programs don't consider them.

Anyway, the article above lists a few programs.  It's also possible to use regular expressions.

Cheers,
Jeff

jalil fallah wrote:
> Dear all ,
> 
> I was wondering if you would mind answering my request.
> How could I access to a software or a database to find tandem repeat
> sequences in a prokaryotic gene ?
> 
> Thank you in advance
> 
> 

-- 
J.W. Bizzaro
Bioinformatics Organization, Inc. (Bioinformatics.Org)
E-mail: jeff at bioinformatics.org
Phone:  +1 978 562 4800
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