Gapped permutation pattern discovery for gene order comparisons

Journal of Computational Biology

Volumn 14, Issue 1, 2007, Pages 45-55

  Parida, Laxmi ^a  

^a IBM T J WATSON RESEARCH CENTER   (United States)

Author keywords

Clusters; Comparative genomics; Data mining; Evolutionary analysis; Labeled trees; Motifs; Pattern discovery; Patterns; Permutation patterns; Whole genome analysis

Indexed keywords

ARTICLE; DNA SEQUENCE; GENE CLUSTER; GENE ORDER; GENETIC ALGORITHM; GENETIC MODEL; GENOME ANALYSIS; MATHEMATICAL ANALYSIS; MOLECULAR PHYLOGENY; PRIORITY JOURNAL;

ALGORITHMS; GENE ORDER; GENES; MODELS, GENETIC; POLYMORPHISM, GENETIC; SEQUENCE ANALYSIS, DNA;

EID: 34047219643     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2006.0103     Document Type: Article

References (16)

1. Aho, A.V., Hopcroft, J.E., and Ullman, J.D. 1983. Data Structure and Algorithms. Addison-Wesley, Boston.
2. Alexandersson, M., Cawley, S., and Pachter, L. 2003. SLAM-cross-species gene finding and alignment with a generalized pair hidden Markov model, 496-502. In Genome Research, Volume 13. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
3. Bergeron, A., Corteel, S., and Raffinot, M. 2002. The algorithmic of gene teams. Proc. WABI 464-476.
4. Bergeron, A., Chauve, C., de Montgolfier, F., et al. 2005. Computing common intervals of k permutations, with applications to modular decomposition of graphs. Proc. ESA 779-790.
5. Booth, K., and Leukar, G. 1976. Testing for the consecutive ones property, interval graphs, and graph planarity using PQ-tree algorithms. J. Comput. Syst. Sci. 13, 335-379.
6. Bray, N., Couronne, O., Dubchak, I., et al. 2003. Strategies and tools for whole-genome alignments, 73-80. In Genome Research, Number 1. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
7. Cosner, M.E., et al. 2000. An empirical comparison of phylogenetic methods on chloroplast gene order data in campanulaceae. Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment, and the Evolution of Gene Families.
8. Eres, R., Landau, G., and Panda, L. 2003. A combinatorial approach to automatic discovery of cluster-patterns. Lect. Notes Bioinfom. 2812, 139-150.
9. He, X., and Goldwasser, M.H. 2004. Identifying conserved gene clusters in the presence of orthologous groups. Proc. ACM (RECOMBo4) 272-280.
10. Heber, S., and Stoye, J. 2001. Finding all common intervals of k permutations. Lect. Notes Comput. Sci. 2089, 207-218.
11. Karim, E., Parida, L., and Lakhotia, A. 2006. Using permutation patterns for content-based phylogeny. Pattern recognition in Bioinformatics. Lect. Notes Bioinfom. 4146, 115-125.
12. Landau, G., Parida, L., and Weimann, O. 2005. Using PQ trees for comparative genomics. Lect. Notes Comput. Sci. 3537, 128-143.
13. Mulley, J., and Holland, P. 2004. Small genome, big insights. Nature 431, 916-917.
14. Parida, L. 2006. Gapped Permutation Patterns for Comparative Genomics. Proceedings of WABI, Algorithms in Bioinformatics. Lect. Notes Bioinform. 4175, 376-387.
15. Schmidt, T., and Stoye, J. 2004. Quadratic time algorithms for finding common intervals in two and more sequences. CPM 3109, 347-358.
16. Uno, T., and Yagiura, M. 2000. Fast algorithms to enumerate all common intervals of two permutations. Algorithmica 26, 290-309.