Mir Asif Iquebal, Sarika and D Kumar
CABiN, ICAR‐IASRI, New Delhi, India
Microsatellites are simple sequence repeats (SSRs), where repeat units are di‐, tri‐ tetra‐ or penta‐nucleotides. A common repeat motif in birds is (AC)n, where the two nucleotides A and C are repeated n number of times (n ranges from 8 to 50). They tend to occur in non‐coding regions of the DNA, but a few human genetic disorders are caused by microsatellite falling in coding regions. There are many tools for mining microsatellite markers.
To learn how to mine simple sequence repeats (SSR) markers in a given DNA sequence.
A number of tools for mining microsatellite markers from genome are available in the public domain. Examples include Repeatmasker (www.repeatmasker.org/; Smit et al., 1996), Sputnik (http://espressosoftware.com/pages/sputnik.jsp; Abajian, 1994) Tandem Repeats Finder (TRF) (http://tandem.bu.edu/trf/trf.html; Benson, 1999), MISA (http://pgrc.ipkgatersleben.de/misa/; Theil et al., 2003), SSRIT (Temnykh et al, 2001), and others.
This can be found at: http://pgrc.ipk‐gatersleben.de/misa/misa.html (Figure 41.1). Requirements for MISA installation are:
Copy the file (Figure 41.2) and save it in a text document as misa.pl.
Copy the misa.ini file (Figure 41.3) and save it in a text document as misa.ini. After installation of misa.pl and misa.ini, microsatellites can be identified using the ./misa.pl FASTAfile.
To mine SSRs from a given sequence:
>sequence
A A T T C G G C A C C A G T A A A T T T T C C C A A A G G T T T C A A A A A T G A A A A T T T T G A T T T T C C T A A T A A T G T T T C T T G C T A T G T T G C T A G T A A C A A G T G G G A A T A A T A A T C T A G T A G A G A C A A C A T G C A A G A A C A C A C C A A A T T A T A A T T T G T G T G T G A A A A C T T T G T C T T T A G A C A A A A G A A G T G A A A A A G C A G G A G A T A T T A C A A C A T T A G C A T T A A T T A T G G T T G A T G C T A T T A A A T C T A A A G C T A A T C A A G C T G C T A A T A C T A T T T C A A A A C T T A G G C A T T C T A A T C C T C C T C A A G C T T G G A A A G A T C C T T T G A A G A A T T G T G C C T T T T C G T A T A A G G T A A T T T T A C C A G C A A G T A T G C C A G A A G C A T T A G A A G C A T T A A C A A A A G G T G A T C C A A A A T T T G C A G A A G A T G G A A T G G T T G G T T C T T C T G G T G A T G C A C A A G A A T G T G A A G A A T A T T T T A A A G C T A C A A C T A T T A A A T A T T C A C C A C T T T C T A A A T T A A A T A T A G A T G T T C A T G A A C T T T C T G A T G T T G G T A G A G C C A T T G T A A G A A A T T T A T T G T A A T A T G T C A T G T C A T A A T G T T A C A T A T C G A A A A G T T T T T A T A G T T T A G T T T G A T A G A C T G T C T G A A T T A T T A T T T T A T T C T T G C T A G T A A A A A T T C G A T T C G T C A C A T T A T G A T C A T C T G T G G T T C A T T T T T C T T T T T T C T A C C T C A A A T G T T A T G T G T G T A T C C C C T C T T A A T T A T T A T A A G A A A A A T A T A T C A T A A A T A T T T G T A C A A G T G T A A T A C T C T T A T C C A A T A T A T A T G T T K G Y C C C C T T C T A A A A A A A A A A A A A A A A A A A A A A A A A A A
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