IMEx: Imperfect Microsatellite Extractor

Mudunuri, Suresh B.; Nagarajaram, Hampapathalu A.

doi:10.1093/bioinformatics/btm097

Cited by 196 publications

(170 citation statements)

References 29 publications

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“…The same approach was previously described in Sputnik, by Katti et al (2001) and Bilgen et al (2004). Imperfect Microsatellite Extractor (IMEx) allows harbouring k mismatches (point mutations) at each of the iterations due to indels or substitutions (Mudunuri and Nagarajaram 2007). Other tools based on the same approach include Poly (Bizzaro and Marx 2003) and SciRoKo (Kofler et al 2007).…”

Section: Mining Tools Based On Sequence Alignmentsmentioning

confidence: 99%

Searching microsatellites in DNA sequences: approaches used and tools developed

Grover

Aishwarya

Sharma

2011

Physiol Mol Biol Plants

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Microsatellite instability associated genomic activities and evolutionary changes have led to a renewed focus on microsatellite research. In last decade, a number of microsatellite mining tools have been introduced based on different computational approaches. The choice is generally made between slow but exhaustive dynamic programming based approaches, or fast and incomplete heuristic methods. Tools based on stochastic approaches are more popular due to their simplicity and added ornamental features. We have performed a comparative evaluation of the relative efficiency of some microsatellite search tools with their default settings. The graphical user interface, the statistical analysis of the output and ability to mine imperfect repeats are the most important criteria in selecting a tool for a particular investigation. However, none of the available tools alone provides complete and accurate information about microsatellites, and a lot depends on the discretion of the user.

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Section: Mining Tools Based On Sequence Alignmentsmentioning

confidence: 99%

Searching microsatellites in DNA sequences: approaches used and tools developed

Grover

Aishwarya

Sharma

2011

Physiol Mol Biol Plants

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“…It is important to mention that the dMAX value can only be set between 0 and 50 for IMEx (24). Our analysis revealed an overall increase in cSSRs percentage with higher dMAX in all the seven Filoviridae genomes (Figure 4).…”

Section: The Effect Of Maximum Distance Allowed Between Any Two Ssrs mentioning

confidence: 74%

“…The microsatellite search was performed using the IMEx software (24). Earlier studies on eukaryotes and E. coli genomes have focused on microsatellites with lengths of 12 bp or more (5), yet due to the smaller size of the Filoviridae family genome, simple and compound microsatellite search using these parameters did not yield any results.…”

Section: Microsatellite Identification and Investigationmentioning

confidence: 99%

Analysis of Simple and Imperfect Microsatellites in Ebolavirus Species and Other Genomes of Filoviridae Family

2015

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Background:Microsatellites have evoked the interest of researchers owing to their applications in different fields such as DNA fingerprinting, genetic mapping, population genetics, forensics, paternity studies and evolution. Objectives: The present study focused on the analysis of simple sequence repeats (SSRs) in genomes of seven species from three genera of the Filoviridae family. Materials and Methods: Genome sequences of seven species from the Filoviridae family were assessed by the National Center for Biotechnology Information (NCBI), microsatellites were extracted using the IMEx software, and statistical analysis was performed Microsoft Office Excel 2007. Results: A total of 516 microsatellites and 14 Compound Simple Sequence Repeats (cSSR) (also known as compound microsatellites) were extracted. Evidently, the conversion of SSRs to cSSR was low. Mononucleotide A/T was the most prevalent followed by dinucleotide AC/CA and trinucleotide AAC/CAA. Highest incidence of SSRs (mon-/di-nucleotide motif) was observed in RNA Dependent RNA Polymerase (RDRP) gene whereas tri-nucleotide motif was maximally localized in nucleoproteins (NP). Conclusions:The salient features of simple and compound microsatellites in Filoviridae family have been highlighted herein. Microsatellite regions with higher mutation rates compared to the rest of the genome play a crucial role in genome evolution by acting as a source of quantitative genetic variation. The SSR mutation rate is known to be affected by motif length, motif sequence, and number of repeats and purity of repetition. The functional role of tandem repeats in viruses, remains to be fully elucidated. However, with the repetitive sequence allegedly acting as a hot spot for recombination, we postulate their involvement in genetic events such as recombination, replication, and repair mechanisms that drive sequence diversity leading to the formation of the genetic basis of adaptation.

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“…To determine the impact of dMAX, 7 genome sequences representing all genera, namely Rose leaf rosette-associated virus (NC_024906), Blackberry vein banding-associated virus (NC_022072), Grapevine leafroll-associated virus 7 (NC_016436), Lettuce chlorosis virus (NC_012909/ NC_012910), Blueberry virus A (NC_018519), Plum bark necrosis stem pitting-associated virus (NC_009992), and Tomato infectious chlorosis virus (FJ815440/FJ815441), were chosen to determine the variability of cSSRs with increasing dMAX. It is noteworthy that the dMAX value can only be set between 0 and 50 for IMEx (Mudunuri and Nagarajaram, 2007). The selected genomes show varied numbers of cSSRs at dMAX 10 ( Table 2).…”

Section: Effect Of Dmax On Cssr Incidencementioning

confidence: 99%

In silico genome-wide identification and analysis of microsatelliterepeats in the largest RNA virus family (Closteroviridae)

George¹,

George²,

Awasthi³

et al. 2016

Turk J Biol

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Microsatellites are known to exhibit ubiquitous presence across all kingdoms of life, including viruses. Members of the family Closteroviridae are the largest RNA viruses and severely affect different agricultural crops worldwide, including citrus, grapevine, and vegetables. Here we identified and systematically analyzed the nature and distribution of both simple and complex microsatellites present in the complete genome of 36 species belonging to Closteroviridae. Our results showed, in all analyzed genomes, that neither genome size nor GC content had any influence on number, relative abundance, or relative density of microsatellites. For each genome, dinucleotide repeats were found to be highly predominant and AT/TA and AG/GA were the two most abundant dinucleotide repeat motifs. Repeats larger than trinucleotide were relatively rare in these viral genomes. Comparative study of occurrence, abundance, and density of microsatellites among available RNA and DNA viral genomes indicated that simple repeats were less abundant in genomes of Closteroviridae. To our knowledge, this is the first analysis of microsatellites occurring in the largest viral genome that infects plants. Characterization of such variations in repeat sequences would be important in deciphering the origin, mutational processes, and role of repeat sequences in viral genomes.

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IMEx: Imperfect Microsatellite Extractor

Abstract: A World Wide Web server and the stand-alone program are available for free access at http://203.197.254.154/IMEX/ or http://www.cdfd.org.in/imex.

Cited by 196 publications

References 29 publications

Searching microsatellites in DNA sequences: approaches used and tools developed

Searching microsatellites in DNA sequences: approaches used and tools developed

Analysis of Simple and Imperfect Microsatellites in Ebolavirus Species and Other Genomes of Filoviridae Family

In silico genome-wide identification and analysis of microsatelliterepeats in the largest RNA virus family (Closteroviridae)

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