BACK TO CONTENTS   |    PDF   |    PREVIOUS   |    NEXT

Title

GMATo: A novel tool for the identification and analysis of microsatellites in large genomes

 

Authors

Xuewen Wang*, Peng Lu & Zhaopeng Luo

 

Affiliation

China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute, NO.2 Fengyang Street, Hi-tech zone, Zhengzhou 450001, China

 

Email

xwwang@ymail.com; *Corresponding author

 

Article Type

Software

 

Date

Received January 01, 2013; Accepted January 13, 2013; Published June 08, 2013

 

Abstract

Simple Sequence Repeats (SSR), also called microsatellite, is very useful for genetic marker development and genome application. The increasing whole sequences of more and more large genomes provide sources for SSR mining in silico. However currently existing SSR mining tools canít process large genomes efficiently and generate no or poor statistics. Genome-wide Microsatellite Analyzing Tool (GMATo) is a novel tool for SSR mining and statistics at genome aspects. It is faster and more accurate than existed tools SSR Locator and MISA. If a DNA sequence was too long, it was chunked to short segments at several Mb followed by motifs generation and searching using Perl powerful pattern match function. Matched loci data from each chunk were then merged to produce final SSR loci information. Only one input file is required which contains raw fasta DNA sequences and output files in tabular format list all SSR loci information and statistical distribution at four classifications. GMATo was programmed in Java and Perl with both graphic and command line interface, either executable alone in platform independent manner with full parameters control. Software GMATo is a powerful tool for complete SSR characterization in genomes at any size.

 

Availability

The soft GMATo is freely available at http://sourceforge.net/projects/gmato/files/?source=navbar or on contact.

 

Keywords

Genome, Microsatellite, SSR, Marker development, Software.

 

Citation

Wang et al.  Bioinformation 9(10): 541-544 (2013)

 

Edited by

P Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.