Searching For Microsatellites Motifs In Ngs Data
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14.0 years ago
Bioch'Ti ★ 1.1k

Hi Guys,

Does anyone have experienced the search of microsatellite motifs in high-throughput sequencing data, such as contigs built from the assembly of 454 data? I would like to screen and eventually map these markers associated to contigs that don't show SNP polymorphism.

Regards, Christopher

next-gen sequencing • 5.0k views
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14.0 years ago
Dave Lunt ★ 2.0k

Not sure this is exactly what you need but Mohammed Noor's lab used a perl script to find microsats in 454 seq fasta file http://www.biology.duke.edu/noorlab/microscan.plx

Looks like it just counts rather than records positions though.

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13.2 years ago

Here are some tools for finding de novo tandem repeats in genomic sequences (not restricted to NGS data).

I can recommend TRF and mreps for speed and ease of use, but have not tried TROLL.

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Thanks for your suggestion of mreps @Casey, it has been very useful to me!

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13.2 years ago

Dear Mr. Ch'ti :P

I just came across SciRoKo, a program that: 'allows for whole genome microsatellite search and investigation.'

There is a command line version for Linux and Mac OsX and a GUI version for Windows.

I'd give it a try!

Cheers

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