Mining Microsatellites...

Question

[Bioch'Ti]

Hi All,

Does anyone know a web-based tool to search for Microsatellites in fasta files, design Primer surrounding each potential marker and perform Blast search?

Regards.

Answer 1

[Darked89]

I did not used it myself, but it seems to have GUI on windows:

http://www.univ-provence.fr/gsite/Local/egee/dir/meglecz/QDD.html

Paper: Meglécz, E., Costedoat, C., Dubut, V., Gilles, A., Malausa, T., Pech, N., Martin, J.F. 2010. QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects. Bioinformatics 2010; Vol. 26,3 : 403-404; doi: 10.1093/bioinformatics/btp670.

Also you may try to search for "sputnik microsatellite". Sputnik was (is?) command based, but since it is very old (1994) a lot of ppl used it and cited. Some web servers may use it in combination with primer3. Still, do not count on a web server capable to take say 500Mbp genome and output all primers flanking microsatelites.

[Bioch'Ti]

Hi Darked89, I tried the iQDD solution to look for microsatellite. This software is perfect as it looks for microsatellites (perfects motif or composite motifs), check for redundancy, and design several couples of primers for each marker. The output file is an HTML that we can easily handle.

[Bioch'Ti]

Hi Darked89,

I tried the iQDD solution to look for microsatellite. This software is perfect as it looks for microsatellites (perfects motif or composite motifs), check for redundancy, and design several couple of primers for each marker. The output file is an HTML that we can easily handle.

[Darked89]

Thanks for reporting that it works :-). Good luck with the probes.

Answer 2

[Mee]

i dont now if it is too late for my answer, but i used MISA, i was developed in 2002 but was updated in 2010

[Sequer]

Its never too late in Biostar :)