[Bio-software] Re: How to find scattered (non-tandem) repeats in DNA sequences?

Mikhail Fursov via bio-soft%40net.bio.net (by mike.fursov from gmail.com)
Tue Apr 6 07:38:06 EST 2010


On Apr 6, 2:54 am, RY Bao <ry_... from yahoo.com> wrote:
> Hello Everybody,
>
> I have a 2kb DNA sequence and would like to analyze the scattered repeats in it, which can be allowed with certain mismatches and may be separated by 1 to hundreds of base pairs. Is there a computer program or Web service available to perform this task ?
>
> Greetings,
> Sunny Bao (Wayne State University, US)

Hi Sunny Bao,

Here is a description of one of the possible solutions for your:

1) Open your sequence in UGENE ( http://ugene.unipro.ru ). Just run
UGENE and use "Open" button or menu.

2) Select "Actions->Analyze->Find repeats" from the main menu

3) Select the repeats parameters: size/identity/distance etc...

4) Push start button and see the repeated regions as annotations
(highlighted regions) to the sequence.

Hope it helps,
Mike.



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