How to extract SSR markers from amino acid sequences ?
Entering edit mode
8.0 years ago
Bara'a ▴ 270

Hi all :)

Does Protein ( Amino acid ) sequences have ( Simple Sequence Repeats ) SSR's in their contents?

I'm wondering if I can extract SSR's from them...

I'm working on a research that requires the extraction of SSR's info as a preprocessing step , and that works fine with me on cDNA sequences using SciRoKo tool, which gives a fairly well structured output format that is easy to be accessed and analyzed by a source code pipeline , as shown in the attached picture.

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But when I attempted to use it with amino acid sequences it throws an exception complaining about the unrecognized contents of the file!!

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I did some search and found IMEX .. I've never used it before , is it good enough to accomplish this task?

I prefer to stick with the SciRoKo tool - for consistency and integration purposes - if anyone can help me to handle that exception ... if NOT , is there any other tools recommended to achieve this task?

Thanks to all who will help.

SSR SciRoKo3.4 amino-acid • 1.7k views

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