Question: Software to identify microsatellites, minisatellites and satellites in a plant genome
0
gravatar for gabri
7 months ago by
gabri50
gabri50 wrote:

Hi All,

I'm annotating a bunch of long contigs from a plant genome.

I'd like to identify microsatellites (2–7 bp), minisatellites (tens of bp) and satellites (hundreds of bp) whitin these contigs.

I know that there are a lots of software to identify the DNA satellite.

I'm thinking to try Tandem Repeats Finder (for minisatellites and satellites) and MISA (for microsatellites).

Do you think that these two software can be enough to catch all the DNA satellite? Are there any better software for these kind of sequences? Is there a specific pipeline?

Thank you for any suggestion!

ADD COMMENTlink written 7 months ago by gabri50
1

You can also have a look on FullSSR for Microsatellite.

ADD REPLYlink written 7 months ago by Nitin Narwade380
1

I have used Phobos with good results.

ADD REPLYlink written 7 months ago by microfuge970
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