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BioMed Research International
Volume 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.

Linked References

  1. S. Leclercq, E. Rivals, and P. Jarne, “Detecting microsatellites within genomes: significant variation among algorithms,” BMC Bioinformatics, vol. 8, article 125, 2007. View at Publisher · View at Google Scholar · View at Scopus
  2. K. G. Lim, C. K. Kwoh, L. Y. Hsu, and A. Wirawan, “Review of tandem repeat search tools: a systematic approach to evaluating algorithmic performance,” Briefings in Bioinformatics, vol. 14, no. 1, Article ID bbs023, pp. 67–81, 2013. View at Publisher · View at Google Scholar · View at Scopus
  3. C. Clayton, “Repetitive elements in parasitic protozoa,” BMC Biology, vol. 8, article 64, 2010. View at Publisher · View at Google Scholar · View at Scopus
  4. B. Wickstead, K. Ersfeld, and K. Gull, “Repetitive elements in genomes of parasitic protozoa,” Microbiology and Molecular Biology Reviews, vol. 67, no. 3, pp. 360–375, 2003. View at Publisher · View at Google Scholar · View at Scopus
  5. J. R. Lupski and P. T. Stankiewicz, Genomic Disorders: The Genomic Basis of Disease, Springer, Berlin, Germany, 2007, http://www.springer.com/gp/book/9781588295590.
  6. G.-F. Richard, A. Kerrest, and B. Dujon, “Comparative genomics and molecular dynamics of DNA repeats in eukaryotes,” Microbiology and Molecular Biology Reviews, vol. 72, no. 4, pp. 686–727, 2008. View at Publisher · View at Google Scholar · View at Scopus
  7. C. Schlotterer, “Evolutionary dynamics of microsatellite DNA,” Chromosoma, vol. 109, no. 6, pp. 365–371, 2000. View at Publisher · View at Google Scholar · View at Scopus
  8. S. B. Mudunuri, A. A. Rao, S. Pallamsetty, and H. A. Nagarajaram, “Comparative analysis of microsatellite detecting software: a significant variation in results and influence of parameters,” in Proceedings of the International Symposium on Biocomputing (ISB '10), ACM, New York, NY, USA, February 2010. View at Publisher · View at Google Scholar · View at Scopus
  9. E. J. Oliveira, J. G. Pádua, M. I. Zucchi, R. Vencovsky, and M. L. C. Vieira, “Origin, evolution and genome distribution of microsatellites,” Genetics and Molecular Biology, vol. 29, no. 2, pp. 294–307, 2006. View at Publisher · View at Google Scholar · View at Scopus
  10. Y. D. Kelkar, N. Strubczewski, S. E. Hile, F. Chiaromonte, K. A. Eckert, and K. D. Makova, “What is a microsatellite: a computational and experimental definition based upon repeat mutational behavior at A/T and GT/AC repeats,” Genome Biology and Evolution, vol. 2, no. 1, pp. 620–635, 2010. View at Publisher · View at Google Scholar · View at Scopus
  11. G. Benson, “Tandem repeats finder: a program to analyze DNA sequences,” Nucleic Acids Research, vol. 27, no. 2, pp. 573–580, 1999. View at Publisher · View at Google Scholar · View at Scopus
  12. A. T. Castelo, W. Martins, and G. R. Gao, “TROLL—tandem repeat occurence locator,” Bioinformatics, vol. 18, no. 4, pp. 634–636, 2002. View at Publisher · View at Google Scholar · View at Scopus
  13. T. Thiel, W. Michalek, R. K. Varshney, and A. Graner, “Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.),” Theoretical and Applied Genetics, vol. 106, no. 3, pp. 411–422, 2003. View at Google Scholar · View at Scopus
  14. R. Kolpakov, G. Bana, and G. Kucherov, “mreps: efficient and flexible detection of tandem repeats in DNA,” Nucleic Acids Research, vol. 31, no. 13, pp. 3672–3678, 2003. View at Publisher · View at Google Scholar · View at Scopus
  15. R. Kofler, C. Schlötterer, and T. Lelley, “SciRoKo: a new tool for whole genome microsatellite search and investigation,” Bioinformatics, vol. 23, no. 13, pp. 1683–1685, 2007. View at Publisher · View at Google Scholar · View at Scopus
  16. M. La Rota, R. V. Kantety, J.-K. Yu, and M. E. Sorrells, “Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley,” BMC genomics, vol. 6, no. 1, article 23, 2005. View at Google Scholar · View at Scopus
  17. L. C. D. Maia, D. A. Palmieri, V. Q. D. Souza, M. M. Kopp, F. I. F. D. Carvalho, and A. Costa de Oliveira, “SSR locator: tool for simple sequence repeat discovery integrated with primer design and PCR simulation,” International Journal of Plant Genomics, vol. 2008, Article ID 412696, 9 pages, 2008. View at Publisher · View at Google Scholar · View at Scopus
  18. S. B. Mudunuri and H. A. Nagarajaram, “IMEx: imperfect microsatellite extractor,” Bioinformatics, vol. 23, no. 10, pp. 1181–1187, 2007. View at Publisher · View at Google Scholar · View at Scopus
  19. X. Wang, P. Lu, and Z. Luo, “GMATo: a novel tool for the identification and analysis of microsatellites in large genomes,” Bioinformation, vol. 9, no. 10, pp. 541–544, 2013. View at Publisher · View at Google Scholar
  20. Z. Ning, A. J. Cox, and J. C. Mullikin, “SSAHA: a fast search method for large DNA databases,” Genome Research, vol. 11, no. 10, pp. 1725–1729, 2001. View at Publisher · View at Google Scholar · View at Scopus
  21. J. Reneker and C.-R. Shyu, “Refined repetitive sequence searches utilizing a fast hash function and cross species information retrievals,” BMC Bioinformatics, vol. 6, article 111, 2005. View at Publisher · View at Google Scholar
  22. M. E. Skinner, A. V. Uzilov, L. D. Stein, C. J. Mungall, and I. H. Holmes, “JBrowse: a next-generation genome browser,” Genome Research, vol. 19, no. 9, pp. 1630–1638, 2009. View at Publisher · View at Google Scholar · View at Scopus
  23. T. Tomov, jqfGridg—Introduction, 2008.
  24. A. A. Holder, “Developments with anti-malarial vaccines,” Annals of the New York Academy of Sciences, vol. 700, no. 1, pp. 7–21, 1993. View at Publisher · View at Google Scholar · View at Scopus