Seeded tree alignment

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 5, Issue 4, 2008, Pages 503-513

  Lozano, Antoni ^a   Pinter, Ron Y ^b   Rokhlenko, Oleg ^c   Valiente, Gabriel ^a   Ziv Ukelson, Michal ^d  

^a UNIVERSITAT POLITÈCNICA DE CATALUNYA   (Spain)

^b TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

^c IBM HAIFA RESEARCH LAB   (Israel)

^d BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

Author keywords

Comparative phylogenetics; RNA structure alignment; Tanglegram layout; Tree matching

Indexed keywords

ALIGNMENT; BIOINFORMATICS; CONFORMAL MAPPING; NUCLEIC ACIDS; PATTERN MATCHING; RNA;

ALGORITHMIC PROBLEMS; COMPARATIVE PHYLOGENETICS; COMPUTATIONAL BIOLOGIES; EFFICIENT ALGORITHMS; LAYOUT PROBLEMS; OPTIMAL TRANSFORMATIONS; ORDERED TREES; PARTIAL MAPPINGS; RNA STRUCTURE ALIGNMENT; RNA STRUCTURES; TANGLEGRAM LAYOUT; TIME ALGORITHMS; TREE ALIGNMENTS; TREE MATCHING; UNORDERED TREES;

APPLICATIONS;

RIBONUCLEASE P; RNA;

ALGORITHM; ARTICLE; GENETICS; METHODOLOGY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

ALGORITHMS; BASE SEQUENCE; EVOLUTION, MOLECULAR; MOLECULAR SEQUENCE DATA; PHYLOGENY; RIBONUCLEASE P; RNA; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA;

EID: 55949121314     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2008.59     Document Type: Article

References (33)

1. 2.5) Time Algorithms for the Subgraph Home-omorphism Problem on Trees," J. Algorithms, vol. 8, pp. 106-112, 1987.
2. B. DasGupta, X. He, T. Jiang, M. Li, J. Tromp, and L. Zhang, "On Distances between Phylogenetic Trees," Proc. Eighth Ann. ACM-SIAM Symp. Discrete Algorithms (SODA '97), pp. 427-436, 1997.
3. J.-F. Dufayard, L. Duret, S. Penel, M. Gouy, F. Rechenmann, and G. Perrière, "Tree Pattern Matching in Phylogenetic Trees: Automatic Search for Orthologs or Paralogs in Homologous Gene Sequence Databases," Bioinformatics, vol. 21, no. 11, pp. 2596-2603, 2005.
4. J. Felsenstein, "Phylip - Phylogeny Inference Package (Version 3.2)," Cladistics, vol. 5, no. 1, pp. 164-166, 1989.
5. U. Fößmeier and M. Kaufmann, "Nice Drawings for Planar Bipartite Graphs," Proc. Third Italian Conf. Algorithms and Complex-ity (CIAC '97), vol. 1203, pp. 122-134, 1997.
6. J.A. Gallian, "A Dynamic Survey of Graph Labeling," Electronic J, Combinatorics, no. DS7, http://www.combinatorics.org/ Surveys/, 2007.
7. K.J. Gardiner, T.L. Marsh, and N.R. Pace, "Ion Dependence of the Bacillus Subtilis RNase P Reaction," J. Biological Chemistry, vol. 260, no. 9, pp. 5415-5419, 1985.
8. E.S. Haas and J.W. Brown, "Evolutionary Variation in Bacterial RNase P RNAs," Nucleic Acids Research, vol. 26, no. 18, pp. 4093-4099, 1998.
9. J.K. Harris, E.S. Haas, D. Williams, D.N. Frank, and J.W. Brown, "New Insight into RNase P RNA Structure from Comparative Analysis of the Archaeal RNA," RNA, vol. 7, no. 2, pp. 220-232, 2001.
10. P. Hugenholtz, "Exploring Prokaryotic Diversity in the Genomic Era," Genome Biology, vol. 3, no. 2, pp. reviews000.1-reviews0003.8, 2002.
11. B.D. James, G.J. Olsen, J. Liu, and N.R. Pace, "The Secondary Structure of Ribonuclease P RNA, the Catalytic Element of a Ribonucleoprotein Enzyme," Cell, vol. 52, no. 1, pp. 19-26, 1988.
12. J. Jansson, N.T. Hieu, and W.-K. Sung, "Local Gapped Subforest Alignment and Its Application in Finding RNA Structural Motifs," J. Computational Biology, vol. 13, no. 3, pp. 702-718, 2006.
13. S.-Y. Le, R. Nussinov, and J.V. Maizel, "Tree Graphs of RNA Secondary Structures and Their Comparisons," Computers in Biomedical Research, vol. 22, no. 5, pp. 461-473, 1989.
14. A. Lozano, R. Pinter, O. Rokhlenko, G. Valiente, and M. Ziv-Ukelson, "Seeded Tree Alignment and Planar Tanglegram Layout," Proc. Seventh Workshop Algorithms in Bioinformatics (WABI '07), vol. 4645, pp. 98-110, 2007.
15. B.L. Maidak, J.R. Cole, T.G. Lilburn, C.T. Parker, P.R. Saxman, J.M. Stredwick, G.M. Garrity, B. Li, G.J. Olsen, S. Pramanik, T.M. Schmidt, and J.M. Tiedje, "The RDP (Ribosomal Database Project) Continues," Nucleic Acids Research, vol. 28, pp. 173-174, 2000.
16. D.W. Matula, "An Algorithm for Subtree Identification," SLAM Rev., vol. 10, pp. 273-274, 1968.
17. 5/2)," Annals Discrete Math., vol. 2, pp. 91-106, 1978.
18. T.M. Nye, P. Lio, and W.R. Gilks, "A Novel Algorithm and Web-Based Tool for Comparing Two Alternative Phylogenetic Trees," Bioinformatics, vol. 22, no. 1, pp. 117-119, 2006.
19. N.R. Pace and J.W. Brown, "Evolutionary Perspective on the Structure and Function of Ribonuclease P, A Ribozyme," J. Bacteriology, vol. 177, no. 8, pp. 1919-1928, 1995.
20. R.D.M. Page, ed., Tangled Trees: Phylogeny, Cospeciation, and Coevolution. The Univ. of Chicago Press, 2002.
21. R.D.M. Page and G. Valiente, "An Edit Script for Taxonomic Classifications," BMC Bioinformatics, vol. 6, p. 208, 2005.
22. R.Y. Pinter, O. Rokhlenko, D. Tsur, and M. Ziv-Ukelson, "Approximate Labelled Subtree Homeomorphism," Proc. 15th Ann. Symp. Combinatorial Pattern Matching (CPM '04), vol. 3109, pp. 59-73, 2004.
23. S.W. Reyner, "An Analysis of a Good Algorithm for the Subtree Problem," SIAM J. Computing, vol. 6, no. 4, pp. 730-732, 1977.
24. R. Shamir and D. Tsur, "Faster Subtree Isomorphism," J. Algorithms, vol. 33, no. 2, pp. 267-280, 1999.
25. H. Shan, K.G. Herbert, W.H. Piel, D. Shasha, and J.T.L. Wang, "A Structure-Based Search Engine for Phylogenetic Databases," Proc. 14th Int'l Conf. Scientific and Statistical Database Management (SSDBM '02), pp. 7-10, 2002.
26. B.A. Shapiro and K. Zhang, "Comparing Multiple RNA Secondary Structures Using Tree Comparisons," Computer Applications in the Biosciences, vol. 6, no. 4, pp. 309-318, 1990.
27. D. Shasha, J.T.-L. Wang, and R. Giugno, "Algorithmics and Applications of Tree and Graph Searching," Proc. 21st ACM SIGACT-SIGMOD-SIGART Symp. Principles of Database Systems (PODS '02), pp. 39-52, 2002.
28. G. Valiente, Algorithms on Trees and Graphs. Springer, 2002.
29. G. Valiente, "Constrained Tree Inclusion," J. Discrete Algorithms, vol. 3, nos. 2-4, pp. 431-447, 2005.
30. G. Valiente, "A Fast Algorithmic Technique for Comparing Large Phylogenetic Trees," Proc. 12th Int'l Symp. String Processing and Information Retrieval (SPIRE '05), vol. 3772, pp. 371-376, 2005.
31. C.R. Woese and N.R. Pace, "Probing RNA Structure, Function, and History by Comparative Analysis," The RNA World, R.F. Gesteland and J.F. Atkins, eds., pp. 91-117, Cold Spring Harbor Laboratory Press, 1993.
32. W.N.W. Zainon and P. Calder, "Visualizing Phylogenetic Trees," Proc. Seventh Australasian User Interface Conf. (AUIC '06), pp. 145-152, 2006.
33. K. Zhang, L. Wang, and B. Ma, "Computing Similarity between RNA Structures," Proc. 10th Ann. Symp. Combinatorial Pattern Matching (CPM '99), vol. 1645, pp. 281-293, 1999.