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BioMed Research International
Volume 2015 (2015), Article ID 394157, 9 pages
http://dx.doi.org/10.1155/2015/394157
Research Article

ProGeRF: Proteome and Genome Repeat Finder Utilizing a Fast Parallel Hash Function

1Department of Computer Science, Federal University of Mato Grosso, 78600-000 Barra do Garcas, MT, Brazil
2Federal Center of Technological Education of Minas Gerais, Belo Horizonte, MG, Brazil
3Department of Parasitology, Federal University of Minas Gerais, 31270-829 Belo Horizonte, MG, Brazil

Received 3 June 2014; Revised 19 January 2015; Accepted 31 January 2015

Academic Editor: Satoru Miyano

Copyright © 2015 Robson da Silva Lopes et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Repetitive element sequences are adjacent, repeating patterns, also called motifs, and can be of different lengths; repetitions can involve their exact or approximate copies. They have been widely used as molecular markers in population biology. Given the sizes of sequenced genomes, various bioinformatics tools have been developed for the extraction of repetitive elements from DNA sequences. However, currently available tools do not provide options for identifying repetitive elements in the genome or proteome, displaying a user-friendly web interface, and performing-exhaustive searches. ProGeRF is a web site for extracting repetitive regions from genome and proteome sequences. It was designed to be efficient, fast, and accurate and primarily user-friendly web tool allowing many ways to view and analyse the results. ProGeRF (Proteome and Genome Repeat Finder) is freely available as a stand-alone program, from which the users can download the source code, and as a web tool. It was developed using the hash table approach to extract perfect and imperfect repetitive regions in a (multi)FASTA file, while allowing a linear time complexity.