Searching For Microsatellites Motifs In Ngs Data

Question

[Bioch'Ti]

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

Answer 1

[Dave Lunt]

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.

Answer 2

[Casey Bergman]

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

• TRF
• mreps
• TROLL

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

[Eric Normandeau]

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

Answer 3

[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