Abstract
Simple sequence repeats (SSRs) are ubiquitous short tandem repeats, which are associated with various regulatory mechanisms and have been found in viral genomes. Herein, we develop MfSAT (Multi-functional SSRs Analytical Tool), a new powerful tool which can fast identify SSRs in multiple short viral genomes and then automatically calculate the numbers and proportions of various SSR types (mono-, di-, tri-, tetra-, penta- and hexanucleotide repeats). Furthermore, it also can detect codon repeats and report the corresponding amino acid.
Highlights
Simple sequence repeats (SSRs) or microsatellites are tandemly repeated tracts consisting of 1-6 base pair long units [1, 2]
In order to efficiently screen viral genome sequences for SSRs, we have developed a new tool called MfSAT
When you run according to the first parameter, the minimum number is three, whereas if you run by use of another parameter, the maximum motif is “hexa”
Summary
Simple sequence repeats (SSRs) or microsatellites are tandemly repeated tracts consisting of 1-6 base pair (bp) long units [1, 2]. Comprehensive analysis of SSRs in 8619 pre-miRNAs indicates SSRs are widely present in these very small non-coding RNA sequences [3]. It has been demonstrated that SSRs can affect gene expression and the corresponding gene products and even cause phenotypic changes or diseases [4, 5]. Computational tools for detection of SSRs and their related information from whole genome sequences are increasing as well [6]. The growing number of analytical tools for SSRs has greatly assisted the understanding of SSRs at the genome-wide level. Our examination of the available tools reveals certain faults. In order to efficiently screen viral genome sequences for SSRs, we have developed a new tool called MfSAT
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