SSRs; STRs and microsatellites - What is the difference? (Dec/02/2010 )

Hi!
In literature I've read that SSRs (Simple Sequence Repeats) mean a repetition of 1-6 basepairs.
For example: AGGAGGAGGAGGAGGAGGAGG

But I have also read the same definition for the Short Tandem Repeats (STRs).

Now I am wondering if there is any difference?

And when do I call it a "microsatellite"? Is a SSR/STR only called "microsatellite" if it has
reached a certain amount of these repetitions?

I hope you can help me.

best regards,
Ikar

There is no difference between the abbreviations.
It is a locus with a sequence of at least tandem repeats (i.e. minimum 2 such as (GC)_n, i.e. a dinucleotide repeat). 1 repeat such as (A)_n is in my opinion no SSR/STR/microsatellite.
Microsatellite is a more traditional name coming from a "satellite" (extra) band when genomic DNA is separated by density gradient centrifugation. In that satellite band, lots of highly repetitive DNA is gathered, with different lengths in repeat number and sequence. Micro- is the smallest fraction with 2-6 repeats and short sequence length.

Ok.Thank you so far.

But I have another question yet:

- a repetition of 2-6 bp is called SSR/STR/microsatellite

I have also read that
- a repetition of 10-50 bp is calles minisatellite
- a repetition of 100-200 bp is a tandem repeat.

What about repetitions of 7-9 bp? Do I call them mini- or microsatellite?
And what about 51 to 99 bp long repetitions?

I don't think that the definitions are that strict...perhaps I'd call them microsatellites too...
Or use another abbreviation: VNTR (variable number tandem repeats)

hobglobin on Thu Dec 2 13:31:18 2010 said:

I don't think that the definitions are that strict...perhaps I'd call them microsatellites too...
Or use another abbreviation: VNTR (variable number tandem repeats)

Hi everyone! what's the best program for finding SSR ?? i'd tried MISA which i find good but there are many others in the literature, what would you recomend??