Empirical Evaluation of in silico Microsatellites Mining Tools Designed Using Nextgen Technology in Crops

Abstract

Microsatellites are found in genome sequences of all prokaryotes and eukaryotes. They are the primary source of studying genetic variations, molecular breeding, gene discovery, disease identification, and hypervariability in a plant's genome. Many web-based and standalone computing tools have been developed to analyze sequence data using next-generation sequencing tools with several new features and objectives. Researchers always need a variety of in silico microsatellite exploring tools to analyze research data apart from extracting them. This evaluation aims to chronologically provide up-todate information on tools and databases designed explicitly to study genome-wide specifications of simple sequence repeats in crop cultivars. The study was conducted to empirically assess these tools and databases to find the next-generation technology used in designing the standalone tool, web interface & relational database. Also, to compare their processing adequateness in terms of features, such as the primer-related information, flanking sequences, statistics information of repeats, coding /non-coding, and other genomic features of the identified motif. This study may help researchers in agriculture to determine the most popular next-generation sequencing tool and technologies used to analyze microsatellite-related features and fill the gap for future applications.