Appreciate if someone can explain the methodology of calculating the microsatellite repeat score or the methodology of calculating the repeat score for simple tandem repeats.
I have no answer for this directly. Please have a look at http://bioinformatics.iyte.edu.tr/index.php?n=Softwares.SiSeeR which will find such repeating sequences.
It is hard to say how to score SSRs, but their length (repeat*motif length) is likely to be important (from a probabilistic point of view). Generally, empirical motif length repeat number cutoffs are used. Sure there are standards (look at the defaults in the software), but whether that is biologically significant is a different question.
Like you, I would be very interested in learning about biological implication and scores derived from that.
Thanks a lot for the reply Prof. Allmer. I'm trying to use the repeat score (in this case I'm planning to use the number of repeats at each identified locus) to analyze the population structure of a Protozoan, using the Structure (v2.3.4) software. Any thoughts on how viable this approach could be in deriving an accurate analysis ?
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