[BiO BB] finding repeat sequences
jeff at bioinformatics.org
Mon Dec 8 13:09:29 EST 2008
There is a nascent article on the topic here (mostly about nomenclature right now):
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.
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
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