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ProGeRF: proteome and genome repeat finder utilizing a fast parallel hash function.

Robson da Silva Lopes¹, Walas Jhony Lopes Moraes¹, Thiago de Souza Rodrigues²

¹Department of Computer Science, Federal University of Mato Grosso, 78600-000 Barra do Garcas, MT, Brazil.

Biomed Research International

|March 27, 2015

Summary

ProGeRF is a new bioinformatics tool for finding repetitive DNA sequences in genomes and proteomes. This user-friendly web tool efficiently identifies exact and approximate repeats, aiding population biology research.

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Novel Sequence Discovery by Subtractive Genomics

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Published on: January 25, 2019

Area of Science:

Bioinformatics
Genomics
Molecular Biology

Background:

Repetitive element sequences serve as crucial molecular markers in population biology.
Genome sequencing necessitates advanced bioinformatics tools for repetitive element extraction.
Existing tools lack comprehensive features for genome-wide repetitive element identification and user-friendly analysis.

Purpose of the Study:

To introduce ProGeRF, a novel web-based tool for extracting repetitive regions from genome and proteome sequences.
To provide an efficient, fast, accurate, and user-friendly platform for analyzing repetitive elements.
To enable exhaustive searches and diverse result visualization for repetitive sequence identification.

Main Methods:

Developed ProGeRF as both a stand-alone program and a web tool.
Utilized a hash table approach for efficient repetitive region extraction.
Implemented algorithms to identify both perfect and imperfect repetitive sequences within (multi)FASTA files with linear time complexity.

Main Results:

ProGeRF successfully extracts repetitive regions from genome and proteome sequences.
The tool offers a user-friendly interface for viewing and analyzing results.
Achieved efficient and accurate identification of repetitive elements, including imperfect matches.

Conclusions:

ProGeRF provides a valuable and accessible resource for researchers studying repetitive elements in genomic and proteomic data.
The tool's efficiency and user-friendliness enhance the analysis of molecular markers in population biology.
ProGeRF addresses limitations of existing bioinformatics tools for repetitive sequence discovery.