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

RY Bao via bio-soft%40net.bio.net (by ry_bao from yahoo.com)
Tue Apr 6 16:19:09 EST 2010


Hi Mike,

Thank you very much! It's working great. I obtained the list of scattered repeats with their positions, length, and distance between the repeats (minimum repeat length = 6bp, repeats identity = 100%, minimum distance between repeats  = 1bp) . I have one quick question. For example, in case of 

1. repeat unit, join(2..9, 1625..1632 )
2. repeat unit, join(3..10, 1995..2002)
3. repeat unit, join(3..9, 1806..1812)
4. repeat unit, join(3..8, 1488..1493)

Those 4 query repeats overlap, however, their target repeats do not overlap at all. Is this because in case of overlapping/nested query repeats, only non-overlapping target repeats are counted? I read the repeat finder plugin section on the instruction page but was not sure. Thanks a lot!

Greetings,
Sunny




________________________________
From: Mikhail Fursov <mike.fursov from gmail.com>
To: bionet-software from moderators.isc.org
Sent: Tue, April 6, 2010 8:38:06 AM
Subject: [Bio-software] Re: How to find scattered (non-tandem) repeats in DNA sequences?

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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