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Old 06-10-2014, 03:35 AM   #1
SDK
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Default Anyone know a program to detect duplicated regions?

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,
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Old 06-19-2014, 05:54 AM   #2
TiborNagy
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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 at 05:54 AM. Reason: misstype
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duplication, mitochondrial genome, mtdna, software

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