AUTOMATIC IDENTIFICATION OF DNA MARKERS BASED ON FEATURES REDUCTION

Carlos M. Travieso, Jordi Solé-Casals, Jesús B. Alonso, Miguel A. Ferrer

Abstract

This paper has implemented a feature reduction based on Independent Components Analysis (ICA) and Principal Component Analysis (PCA) for an automatic supervised identification system of Pejibaye palm DNA markers, using an Artificial Neural Network (ANN) as classifier; obtaining 100% for the classes’ identification. The biochemical parameterization proposed, based on 89 RAPD primer markers applied on haplotypes of Pejibaye races, has correctly been proved for its reduction. The computational times have been studied, obtaining results in real time for test mode. Finally the interesting combination of these techniques (biochemical and computational), gives rise to a formulation of an inexpensive and handy method of origin denomination plant certification.

References

  1. Henderson, A., 2000. Bactris (Palmae). Flora Neotropica Monograph 79, pp: 1-181.
  2. Mora-Urpí, J., Arroyo. C., 1996, Sobre origen y diversidad en pejibaye. Serie Técnica Pejibaye (Guilielma). Boletín Informativo. Editorial de la Universidad de Costa Rica. 5(1): 18-25.
  3. Mora-Urpí, J., Clement C. and Patiño. V., 1993. Diversidad Genética en Pejibaye: I. Razas e Híbridos. IV Congreso Internacional sobre Biología, Agronomía e Industrialización del Pijuayo. Universidad de Costa Rica. p. 11-20.
  4. Dellaporta, S.L., Wood, J., Hick, J.B., 1983. Plant DNA minipreparation. Version II: Plant Mol. Biol. Rep. 1, pp 19-21.
  5. Ferrer, M., Eguiarte, L.E., Montana, C., 2004. Genetic structure and outcrossing rates in Flourensia cernua (Asteraceae) growing at different densities in the South-western Chihuahuan Desert. Annals of Botany 94, pp 419-426.
  6. Mattos, L., 1992. Diferenciación Taxonómica de Diez Razas de Pejibaye Cultivado (Bactris(Guilielma) Gasipaes Kunth) y su relación con otras Especies de Bactris. Magister Scientiae, Universidad de Costa Rica. pp 197.
  7. Porebski, S., Grant, L., Baun, B., 1997. Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Molecular Biology Reporter 15, pp: 8-15.
  8. Ravishankar, K. V., Anand, L., Dinesh M.R., 2000. Assessment of genetic relatedness among mango cultivars of India using RAPD markers. Journal of Horticultural Sci. & Biotechnology, 75, pp 198-201.
  9. Clement, C.R., Aguiar, J., Arkcoll, D.B., Firmino, J., Leandro, R., 1989. Pupunha brava (Bactris dahlgreniana Glassman): progenitora da pupunha (Bactris gasipaes H.B.K.). Boletim do Museu Paraense Emilio Goeldi, Botánica, 5(1) pp 39-55.
  10. De la Torre, F., 2008. A Least-Squares Unified View of PCA, LDA, CCA and Spectral Graph Methods. Tech. report CMU-RI-TR-08-29, Robotics Institute, Carnegie Mellon University, May.
  11. Jutten, C. Herault, J., 1991. Blind separation of sources, Part 1: an adaptive algorithm based on neuromimetic architecture”, Signal Processing (Elsevier), Vol. 24 , Issue 1.
  12. Hyvärinen, A., Karhunen, J., Oja, E., Independent Component Analysis, New York, USA: John Wiley & Sons, 2001
  13. Jolliffe I.T. 2002. Principal Component Analysis, Series: Springer Series in Statistics, 2nd ed., Springer, NY.
  14. Sanchez-Poblador, V. Monte Moreno, E., Solé-Casals, J., 2004. ICA as a preprocessing technique for Classification, ICA 2004, Granada, Spain,. Lecture Notes in Computer Science, Springer-Verlag Volume 3195/2004.
  15. Cardoso, J. F., 1999. High-Order Contrasts for Independent Component Analysis, Neural Computation, 11(1):157--192,
  16. Bishop, C.M., 1995. Neural Networks for Pattern Recognition, Oxford University Press.
  17. Hush, D.R., Horne, B.G., 1993. Progress in supervised neural networks”, IEEE Signal Processing Magazine, 10 (1), pp. 8-39.
Download


Paper Citation


in Harvard Style

Travieso C., Solé-Casals J., Alonso J. and Ferrer M. (2010). AUTOMATIC IDENTIFICATION OF DNA MARKERS BASED ON FEATURES REDUCTION . In Proceedings of the Third International Conference on Bio-inspired Systems and Signal Processing - Volume 1: BIOSIGNALS, (BIOSTEC 2010) ISBN 978-989-674-018-4, pages 347-352. DOI: 10.5220/0002335503470352


in Bibtex Style

@conference{biosignals10,
author={Carlos M. Travieso and Jordi Solé-Casals and Jesús B. Alonso and Miguel A. Ferrer},
title={AUTOMATIC IDENTIFICATION OF DNA MARKERS BASED ON FEATURES REDUCTION},
booktitle={Proceedings of the Third International Conference on Bio-inspired Systems and Signal Processing - Volume 1: BIOSIGNALS, (BIOSTEC 2010)},
year={2010},
pages={347-352},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0002335503470352},
isbn={978-989-674-018-4},
}


in EndNote Style

TY - CONF
JO - Proceedings of the Third International Conference on Bio-inspired Systems and Signal Processing - Volume 1: BIOSIGNALS, (BIOSTEC 2010)
TI - AUTOMATIC IDENTIFICATION OF DNA MARKERS BASED ON FEATURES REDUCTION
SN - 978-989-674-018-4
AU - Travieso C.
AU - Solé-Casals J.
AU - Alonso J.
AU - Ferrer M.
PY - 2010
SP - 347
EP - 352
DO - 10.5220/0002335503470352