1 (1) 2017, AUGUST,2017
Survey, analysis and functionality of microsatellite identification tools for the development of microsatellite or simple sequence repeat (SSR) markers for crop improvement
Author: M.K. Rangari , S.K. Rangari and A.A.Ramteke
Total sixteen tools were surveyed for their functionality in particular for the development of microsatellite loci. The surveyed tools are viz., ATR Hunter, IMEx, Misa, Mreps, Msatfinder, Poly, Repeat, Masker, SciRoKoCo, Sputnik,SSRF, SSRLocator, SSRIT, STAR, STRING, TRF, TROLL. The comparative analysis of the features of these tools is presented in paper. Hence, by comparing various features of the microsatellite identification tools it is concluded that a significant difference in the availability of various features and options was observed in these tools. MISA, SSRIT, Sputnik are among the mostly widely used software’s for microsatellite identification in various crops e.g. Rice, Wheat, Barley and Maize. Hence, it is important for the researcher to choose the parameters carefully before using the bioinformatic tool to identify the microsatellite markers. Customized search criteria may prove better than the default settings while using these tools.
Keywords: Bioinformatic tool, survey, microsatellite, marker, loci