A study of compression-based methods for the analysis of barcode sequences

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 7845 LNBI, Issue , 2013, Pages 105-116

  La Rosa, Massimo ^a   Fiannaca, Antonino ^a   Rizzo, Riccardo ^a   Urso, Alfonso ^a  

^a CNR   (Italy)

Author keywords

Barcode DNA; Compression Based distances; Phylogenetic trees; Universal Similarity Metric

Indexed keywords

COMPRESSION-BASED DISTANCES; CYTOCHROME C OXIDASE; EVOLUTIONARY DISTANCE; MITOCHONDRIAL GENES; NUCLEOTIDE SEQUENCES; PHYLOGENETIC TREES; SEQUENCE ALIGNMENTS; UNIVERSAL SIMILARITY METRIC;

ARTIFICIAL INTELLIGENCE; BAR CODES;

BIOINFORMATICS;

EID: 84883344649     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-38342-7_10     Document Type: Conference Paper

References (31)

1. Savolainen, V., Cowan, R.S., Vogler, A.P., Roderick, G.K., Lane, R.: Towards writing the encyclopaedia of life: an introduction to DNA barcoding. Philos. Trans. R. Soc. Lond. B Biol. Sci. 360, 1805-1811 (2005)
2. Hebert, P.D.N., Cywinska, A., Ball, S.L., de Waard, J.R.: Biological identifications through DNA barcodes. Proc. Biol. Sci. 270, 313-321 (2003)
3. Hebert, P.D.N., Ratnasingham, S., de Waard, J.R.: Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc. Biol. Sci. 270(suppl. 1), 96-99 (2003)
4. Costa, F.O., Carvahlo, G.R.: The Barcode of Life Initiative: synopsis and prospective societal impacts of DNA barcoding of fish. Genomics, Society and Policy 3, 29-40 (2007)
5. Hebert, P.D.N., Stoeckle, M.Y., Zemlak, T.S., Francis, C.M.: Identification of Birds through DNA Barcodes. PLoS Biol. 2(10), e312 (2004)
6. Smith, M.A., Fisher, B.L., Hebert, P.D.N.: DNA barcoding for effective biodiversity assessment of a hyperdiverse arthropod group: the ants of Madagascar. Phil. Trans. R. Soc. B 360, 1825-1834 (2005)
7. Hajibabaei, M., Janzen, D.H., Burns, J.M., Hallwachs, W., Hebert, P.D.N.: DNA barcodes distinguish species of tropical Lepidoptera. PNAS 103(4), 968-971 (2006)
8. Ratnasingham, S., Hebert, P.D.N.: BOLD: The Barcode of Life Data System. Molecular Ecology Notes 7, 355-364 (2007)
9. Li, M., Chen, X., Li, X., Ma, B., Vitanyi, P.M.B.: The Similarity Metric. IEEE T. Inform. Theory 50(12), 3250-3264 (2004)
10. Li, M., Vitanyi, P.M.B.: An Introduction to Kolmogorov Complexity and its Applications, 2nd edn. Springer, New York (1997)
11. Makarenkov, V., Kevorkov, D., Legendre, P.: Phylogenetic network construction approaches. Applied Mycology and Biotechnology 6, 61-97 (2006)
12. Cilibrasi, R., Vitanyi, P.M.B.: Clustering by Compression. IEEE T. Inform. Theory 51(4), 1523-1545 (2005)
13. Li, M., Badger, J.H., Chen, X., Kwong, S., Kearney, P., Zhang, H.: An information-based sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics 17(2), 149-154 (2001)
14. Chen, X., Kwong, S., Li, M.: A compression algorithm for DNA sequences. IEEE Engineering in Medicine and Biology Magazine 20(4), 61-66 (2001)
15. Ferragina, P., Giancarlo, R., Greco, V., Manzini, G., Valiente, G.: Compression-based classification of biological sequences and structures via the Universal Similarity Metric: Experimental assessment. BMC Bioinformatics 8(252) (2007)
16. van Rijsbergen, C.J.: Information Retireval. Butterworths, London (1979)
17. Robinson, D.F., Foulds, L.R.: Comparison of phylogenetic trees. Mathematical Biosciences 53(1), 131-147 (1981)
18. La Rosa, M., Rizzo, R., Urso, A., Gaglio, S.: Comparison of Genomic Sequences Clustering Using Normalized Compression Distance and Evolutionary Distance. In: Lovrek, I., Howlett, R.J., Jain, L.C. (eds.) KES 2008, Part III. LNCS (LNAI), vol. 5179, pp. 740-746. Springer, Heidelberg (2008)
19. La Rosa, M., Gaglio, S., Rizzo, R., Urso, A.: Normalised compression distance and evolutionary distance of genomic sequences: comparison of clustering results. Int. J. Knowledge Engineering and Soft Data Paradigms 1(4), 345-362 (2009)
20. Grumbach, S., Tahi, F.: A new challenge for compression algorithms: genetic sequences. J. Information Processing and Management 30(6), 866-875 (1994)
21. Ziv, J., Lempel, A.: A universal algorithm for sequential data compression. IEEE Trans. Inform. Theory 23(3), 337-343 (1977)
22. Nei, M., Kumar, S.: Molecular Evolution and Phylogenetics. Oxford University Press, New York (2000)
23. Sneath, P.H.A., Sokal, R.R.: Numerical Taxonomy: The Principles and Practice of Numerical Classification. W.H. Freeman, San Francisco (1973)
24. Saitou, N., Nei, M.: The Neighbor-Joining Method: A New Method for Reconstructing Phylogenetic Trees. Mol. Biol. Evol. 4(4), 406-425 (1987)
25. Kimura, M.: Estimation of evolutionary distances between homologous nucleotide sequences. Proc. Natl. Acad. Sci. 78, 454-458 (1981)
26. Tajima, F., Nei, M.: Estimation of evolutionary distance between nucleotide sequences. Molecular Biology and Evolution 1, 269-285 (1984)
27. Tamura, K., Nei, M.: Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution 10, 512-526 (1993)
28. Atallah, M.J., Blanton, M.: Algorithms and Theory of Computation Handbook. CRC Press LLC (1999)
29. Nye, T.M.W., Liò, P., Gilks, W.R.: A novel algorithm and web-based tool for comparing two alternative phylogenetic trees. Bioinformatics 22(1), 117-119 (2006)
30. Soria-Carrasco, V., Talavera, G., Igea, J., Castresana, J.: The K tree score: quantification of differences in the relative branch length and topology of phylogenetic trees. Bioinformatics 23(21), 2954-2956 (2007)
31. Kuhner, M.K., Felsenstein, J.: A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol. 11, 459-468 (1994)