Abstract
Microsatellites are ubiquitous short tandem repeats found in all known genomes and are known to play a very important role in various studies and fields including DNA fingerprinting, paternity studies, evolutionary studies, virulence and adaptation of certain bacteria and viruses etc. Due to the sequencing of several genomes and the availability of enormous amounts of sequence data during the past few years, computational studies of microsatellites are of interest for many researchers. In this context, we developed a software tool called Imperfect Microsatellite Extractor (IMEx), to extract perfect, imperfect and compound microsatellites from genome sequences along with their complete statistics. Recently we developed a user-friendly graphical-interface using JAVA for IMEx to be used as a stand-alone software named G-IMEx. G-IMEx takes a nucleotide sequence as an input and the results are produced in both html and text formats. The Linux version of G-IMEx can be downloaded for free from http://www.cdfd.org.in/imex.
Highlights
Microsatellites, known as Simple Sequence Repeats (SSRs) or Short Tandem Repeats (STRs), are tandem repetitions of a nucleotide motif of size 1-6 bp
A software tool that can extract all types of microsatellites with greater sensitivity and provides flexible options to analyze the repeats detected is the need of the day
Few tools [6,7,8,9] exist in the public domain for extracting microsatellites from genome sequences, but many of them suffer from certain lacunae interms of their features and their efficiency
Summary
Background: Microsatellites, known as Simple Sequence Repeats (SSRs) or Short Tandem Repeats (STRs), are tandem repetitions of a nucleotide motif of size 1-6 bp. Analysis of these microsatellites is important to understand their role in various studies. Computational analysis is a better alternative to the time-consuming and money-intensive traditional wet lab microsatellite studies.
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