Which is the best software to filter SSR motifs from an assembled fasta file?

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Abhijeet Singh

If it is a fasta file and assembled, it can't be in GBs. There is something wrong. Check before your proceed.

Anuj Kumar

Dear Nazima, You may consider GMATA tool. Article GMATA: An Integrated Software Package for Genome-Scale SSR M...

Nazima Habibi

Thanks Anuj Kumar.. I tried using GMATA and was able to filter the SSR motifs... Moving on to the next step that is primer designing

Mohammadreza Rezaei

You can also use the offline version of Misa. Click on "Download Sourcecode" in this page:

https://webblast.ipk-gatersleben.de/misa/

You should run it under perl. For example:

perl ./misa.pl

Regards

Lara Radovic

SciRoKo software, it also can extract flanking regions, and has an add on for creating primers