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A Robust Polymerase Chain Reaction-based Assay for Quantifying Cytosine-guanine-guanine Trinucleotide Repeats in Fragile X Mental Retardation-1 Gene

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RepeatAnalyzer: a tool for analysing and managing short-sequence repeat data.

Helen N Catanese¹, Kelly A Brayton², Assefaw H Gebremedhin³

¹School of Electrical Engineering and Computer Science, Washington State University, Pullman, Washington, 99164, USA.

|June 5, 2016

Summary

This summary is machine-generated.

RepeatAnalyzer software accurately tracks and catalogs short-sequence repeats (SSRs) for strain identification. This tool aids genetic diversity analysis and corrects errors in published SSR data.

Keywords:

Anaplasma marginale Genetic diversity Genotyping Knuth-Morris-Pratt algorithm Msp1a RepeatAnalyzer Short sequence repeat (SSR)Software tool Visualization

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Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Area of Science:

Genomics
Bioinformatics
Microbial genetics

Background:

Short-sequence repeats (SSRs) are DNA sequences found in prokaryotes and eukaryotes.
Tracking and cataloging SSRs for strain genotyping is challenging due to manual errors and diverse research groups.
Heterogeneous SSRs offer patterns for effective strain identification.

Purpose of the Study:

To develop RepeatAnalyzer, a software tool for tracking, managing, analyzing, and cataloging SSRs and genotypes.
To provide novel metrics for measuring regional genetic diversity and visualize SSR/genotype distribution.
To validate RepeatAnalyzer's accuracy and identify potential errors in existing SSR literature.

Main Methods:

Developed RepeatAnalyzer software for SSR and genotype analysis.
Utilized Anaplasma marginale as a model species for validation.
Validated repeat identification against 21 publications and 380 isolates.

Main Results:

RepeatAnalyzer demonstrated accurate genotyping for all tested SSRs and genotypes.
The tool identified numerous errors in published SSR data, including misreported SSRs and naming inconsistencies.
Analysis revealed normal distribution of genotype lengths and power-law-like SSR frequencies in A. marginale.

Conclusions:

RepeatAnalyzer is a robust tool for SSR storage, management, and analysis across species.
Genotype lengths in A. marginale follow a normal distribution, while SSR frequencies follow a power-law-like distribution.
The most common edit distance between repeats was unexpectedly high (five or six).