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Searching For Microsatellites Motifs In Ngs Data

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
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updated by Ram Ram • written by Bioch'Ti • Bioch'Ti

3 answers

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.

• 156 views • link
updated by Ram Ram • written by Dave Lunt • Dave Lunt

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.

• 130 views • link
updated by Ram Ram • written by Casey Bergman Casey Bergman

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

• 0 views • link
written by Eric Normandeau Eric Normandeau

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

• 0 views • link
updated by Ram Ram • written by Eric Normandeau Eric Normandeau

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