Basic Applied Bioinformatics

CHAPTER 41 In Silico Mining of Simple Sequence Repeats (SSR) Markers

Mir Asif Iquebal, Sarika and D Kumar

CABiN, ICAR‐IASRI, New Delhi, India

41.1 INTRODUCTION

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.

41.2 OBJECTIVE

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.

41.3 MISA (MICROSATELLITE IDENTIFICATION TOOL)

This can be found at: http://pgrc.ipk‐gatersleben.de/misa/misa.html (Figure 41.1). Requirements for MISA installation are:

1. Windows XP operating system (minimum 512 MB RAM, Pentium IV processor), or Linux‐based system.
2. Perl is to be installed.

FIGURE 41.1 MISA homepage.

41.3.1 MISA installation

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