How to extract SSR markers from amino acid sequences ?
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6.9 years ago
Bara'a ▴ 250

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 ( http://kofler.or.at/bioinformatics/SciRoKo/ ) , 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 .

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

I did some search and found this : ( http://14.139.82.200/IMEX/index.html ) .. 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 .

 
 
SciRoKo 3.4 amino acid SSR • 1.5k views
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