Sequence transformation to a complex signature form for consistent phylogenetic tree using Extensible Markov Model

2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2010

Volumn , Issue , 2010, Pages 61-68

  Kotamarti, Rao M ^a   Hahsler, Michael ^a   Raiford, Douglas W ^b   Dunham, Margaret H ^a  

^a Southern Methodist University   (United States)

^b UNIVERSITY OF MONTANA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

16S RRNA; BURKHOLDERIA; DISTANCE MATRICES; DISTANCE METRICS; EXTENSIBLE MARKOV MODELS; FOUR-POINT; MULTIPLE GENES; NEIGHBOR-JOINING ALGORITHM; PHYLOGENETIC ANALYSIS; PHYLOGENETIC TREE ANALYSIS; PHYLOGENETIC TREES; SEQUENCE DATA;

ALIGNMENT; ARTIFICIAL INTELLIGENCE; BIOLOGY; CLUSTERING ALGORITHMS; INFERENCE ENGINES; MARKOV PROCESSES; RNA;

BIOINFORMATICS;

EID: 77955600603     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CIBCB.2010.5510472     Document Type: Conference Paper

References (32)

1. J. E. Clarridge, "Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases." Clin Microbiol Rev, vol. 17, no. 4, pp. 840-62, table of contents, Oct 2004. [Online]. Available: http://dx.doi.org/10.1128/CMR.17.4.840- 862.2004
2. W. G. Weisburg, S. M. Barns, D. A. Pelletier, and D. J. Lane, "16S ribosomal DNA amplification for phylogenetic study." J Bacteriol, vol. 173, no. 2, pp. 697-703, Jan 1991.
3. R. J. Case, Y. Boucher, I. Dahllf, C. Holmstrm, W. F. Doolittle, and S. Kjelleberg, "Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies." Appl Environ Microbiol, vol. 73, no. 1, pp. 278-288, Jan 2007. [Online]. Available: http://dx.doi.org/10.1128/AEM.01177-06
4. T. G. Lilburn and G. M. Garrity, "Exploring prokaryotic taxonomy." Int J Syst Evol Microbiol, vol. 54, no. Pt 1, pp. 7-13, Jan 2004.
5. D. Moreira and H. Philippe, "Molecular phylogeny: pitfalls and progress." Int Microbiol, vol. 3, no. 1, pp. 9-16, Mar 2000.
6. M. H. Dunham, Y. Meng, and J. Huang, "Extensible markov model," in Proc. Fourth IEEE International Conference on Data Mining ICDM '04, 1-4 Nov. 2004, pp. 371-374.
7. R. M. Kotamarti, D. W. Raiford, M. Hahsler, Y. Wang, M. McGee, and M. H. Dunham, "Targeted genomic signature profiling with quasi-alignment statistics," COBRA Preprint Series, November 2009. [Online]. Available: http://biostats.bepress.com/cobra/ps/art63
8. Y. Meng and M. H. Dunham, "Online mining of risk level of traffic anomalies with user s feedbacks," Granular Computing, 2006 IEEE International Conference, pp. 176-181, 2006.
9. Y. Meng, M. H. Dunham, M. Marchetti, and H. Jie, "Rare event detection in a spatiotemporal environment," Granular Computing, 2006 IEEE International Conference, pp. 629-634, 2006.
10. M. T. Bergey's, Ed., Manual of Systematic Bacteriology, Vol. 15 (20012009) 2nd edn, 2nd ed. New York: Springer Verlag, 2009.
11. S. Karlin and S. F. Altschul, "Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes." Proc Natl Acad Sci U S A, vol. 87, no. 6, pp. 2264-2268, Mar 1990.
12. S. Vinga and J. Almeida, "Alignment-free sequence comparison-a review." Bioinformatics, vol. 19, no. 4, pp. 513-523, Mar 2003.
13. J. L. Thorne and H. Kishino, "Freeing phylogenies from artifacts of alignment." Mol Biol Evol, vol. 9, no. 6, pp. 1148-1162, Nov 1992.
14. R. Shahid, S. Bertazzon, M. Knudtson, and W. Ghali, "Comparison of distance measures in spatial analytical modeling for health service planning," BMC Health Services Research, vol. 9, no. 1, p. 200, 2009. [Online]. Available: http://www.biomedcentral.com/1472-6963/9/200
15. L. Wang and T. Jiang, "On the complexity of multiple sequence alignment." J Comput Biol, vol. 1, no. 4, pp. 337-348, 1994.
16. J. D. Thompson, D. G. Higgins, and T. J. Gibson, "CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice." Nucleic Acids Res, vol. 22, no. 22, pp. 4673-4680, Nov 1994.
17. R. C. Edgar, "MUSCLE: a multiple sequence alignment method with reduced time and space complexity." BMC Bioinformatics, vol. 5, p. 113, Aug 2004. [Online]. Available: http://dx.doi.org/10.1186/1471-2105-5-113
18. S. Henikoff and J. G. Henikoff, "Amino acid substitution matrices from protein blocks." Proc Natl Acad Sci U S A, vol. 89, no. 22, pp. 10 915-10 919, Nov 1992.
19. M. O. Dayhoff, R. M. Schwartz, and B. C. Orcutt, "A model of evolutionary change in proteins," Atlas of protein sequence and structure, vol. 5, no. suppl 3, pp. 345-351, 1978.
20. S. Altschul, W. Gish, W. Miller, E. Myers, and D. Lipman, "Basic local alignment search tool," J. Mol. Biol., vol. 215, pp. 403-410, 1990.
21. S. F. Altschul, T. L. Madden, A. A. Schffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman, "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs." Nucleic Acids Res, vol. 25, no. 17, pp. 3389-3402, Sep 1997.
22. [Online]. Available: http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi
23. L. Vial, M.-C. Groleau, V. Dekimpe, and E. Dziel, "Burkholderia diversity and versatility: an inventory of the extracellular products." J Microbiol Biotechnol, vol. 17, no. 9, pp. 1407-1429, Sep 2007.
24. H. H. Otu and K. Sayood, "A new sequence distance measure for phylogenetic tree construction." Bioinformatics, vol. 19, no. 16, pp. 2122-2130, Nov 2003.
25. P. Buneman, "The recovery of trees from measures of dissimilarity," Mathematics the the Archeological and Historical Sciences, p. 387395, 1971.
26. O. Gascuel, "BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data." Mol Biol Evol, vol. 14, no. 7, pp. 685-695, Jul 1997.
27. J. Felsenstein, "PHYLIP (phylogeny inference package), version 3.57 c," Seattle: University of Washington, 1995.
28. B. Nron, H. Mnager, C. Maufrais, N. Joly, J. Maupetit, S. Letort, S. Carrere, P. Tuffery, and C. Letondal, "Mobyle: a new full web bioinformatics framework." Bioinformatics, vol. 25, no. 22, pp. 3005-3011, Nov 2009. [Online]. Available: http://dx.doi.org/10.1093/bioinformatics/btp493
29. T. Z. DeSantis, P. Hugenholtz, N. Larsen, M. Rojas, E. L. Brodie, K. Keller, T. Huber, D. Dalevi, P. Hu, and G. L. Andersen, "Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB." Appl Environ Microbiol, vol. 72, no. 7, pp. 5069-5072, Jul 2006. [Online]. Available: http://dx.doi.org/10.1128/AEM.03006-05
30. D. R. Stothard, J. B. Clark, and P. A. Fuerst, "Ancestral divergence of Rickettsia bellii from the spotted fever and typhus groups of Rickettsia and antiquity of the genus Rickettsia." Int J Syst Bacteriol, vol. 44, no. 4, pp. 798-804, Oct 1994.
31. N. Saitou and M. Nei, "The neighbor-joining method: a new method for reconstructing phylogenetic trees." Mol Biol Evol, vol. 4, no. 4, pp. 406-425, Jul 1987.
32. I. Dahllf, H. Baillie, and S. Kjelleberg, "rpoB-based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity." Appl Environ Microbiol, vol. 66, no. 8, pp. 3376-3380, Aug 2000.