Anyone know a program to detect duplicated regions?

SDK

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Join Date: Jan 2014

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#1

Anyone know a program to detect duplicated regions?

06-10-2014, 03:35 AM

Hi All,

I'm working with on generating denovo mtDNA genomes for many species of an invertebrate taxa of the same genus. These critters have a duplicated non-coding region (~800bp) separated by ~6000bp, the problem is that the non-coding region is different in every species. Since this is not a tandem repeat, and is quite large, the microsatellite finding programs are of no use. Anyone know a program that can find these large duplicated regions?

Cheers,
Tags: duplication, mitochondrial genome, mtdna, software
TiborNagy

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Join Date: Mar 2010

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06-19-2014, 05:54 AM

Why do not use Blast? If the query and the database are the same, it will find all the duplicated regions.

Last edited by TiborNagy; 06-19-2014, 05:54 AM. Reason: misstype
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Anyone know a program to detect duplicated regions?

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