Seeded tree alignment and planar tanglegram layout

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

Volumn 4645 LNBI, Issue , 2007, Pages 98-110

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

^a UNIVERSITAT POLITÈCNICA DE CATALUNYA   (Spain)

^b TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

^c TEL AVIV UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; COMPUTATIONAL METHODS; PATTERN MATCHING; POLYNOMIALS; PROBLEM SOLVING; RNA;

COMPUTATIONAL BIOLOGY; ELEMENTARY EDIT OPERATIONS; OPTIMAL TRANSFORMATION; TREE ALIGNMENT;

TREES (MATHEMATICS);

EID: 37249043167     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-74126-8_10     Document Type: Conference Paper

References (25)

1. 2.5) time algorithms for the subgraph homeomorphism problem on trees. J. Algorithms 8, 106-112 (1987)
2. DasGupta, B., et al.: On distances between phylogenetic trees. In: Proc. 8th Annual ACM-SIAM Symp. Discrete Algorithms, pp. 427-436. ACM Press, New York (1997)
3. Felsenstein, J.: Phylip - phylogeny inference package. Cladistics 5, 164-166 (1989)
4. Gardiner, K.J., Marsh, T.L., Pace, N.R.: Ion dependence of the bacillus subtilis rnase p reaction. J. Biol. Chem. 260, 5415-5419 (1985)
5. Haas, E.S., Brown, J.W.: Evolutionary variation in bacterial RNase P RNAs. Nucleic Acids Res. 26, 4093-4099 (1998)
6. Harris, J.K., et al.: New insight into RNase P RNA structure from comparative analysis of the archaeal RNA. RNA 7, 220-232 (2001)
7. James, B.D., et al.: The secondary structure of ribonuclease P RNA, the catalytic element of a ribonucleoprotein enzyme. Cell 52, 19-26 (1988)
8. Jansson, J., Hieu, N.T., Sung, W.-K.: Local gapped subforest alignment and its application in fnding RNA structural motifs. J. Comput. Biol. 13, 702-718 (2006)
9. Le, S.-Y., Nussinov, R., Maizel, J.V.: Tree graphs of RNA secondary structures and their comparisons. Comput. Biomed. Res. 22, 461-473 (1989)
10. Maidak, B.L., et al.: The RDP (Ribosomal Database Project) continues. Nucleic Acids Res. 28, 173-174 (2000)
11. 5/2). Ann. Discrete Math. 2, 91-106 (1978)
12. Nye, T.M., Lio, P., Gilks, W.R.: A novel algorithm and web-based tool for comparing two alternative phylogenetic trees. Bioinformatics 22, 117-119 (2006)
13. Pace, N.R., Brown, J.W.: Evolutionary perspective on the structure and function of ribonuclease P, a ribozyme. J. Bacteriol. 177, 1919-1928 (1995)
14. Page, R.D.M. (ed.): Tangled Trees: Phylogeny, Cospeciation, and devolution. The University of Chicago Press, Chicago (2002)
15. Page, R.D.M., Valiente, G.: An edit script for taxonomic classifications. BMC Bioinformatics 6, 208 (2005)
16. Pinter, R.Y., et al.: Approximate labelled subtree homeomorphism. In: Sahinalp, S.C., Muthukrishnan, S.M., Dogrusoz, U. (eds.) CPM 2004. LNCS, vol. 3109, pp. 59-73. Springer, Heidelberg (2004)
17. Reyner, S.W.: An analysis of a good algorithm for the subtree problem. SIAM J. Comput. 6, 730-732 (1977)
18. Shamir, R., Tsur, D.: Faster subtree isomorphism. J. Alg. 33, 267-280 (1999)
19. Shan, H., Herbert, K.G., Piel, W.H., Shasha, D., Wang, J.T.L.: A structure-based search engine for phylogenetic databases. In: SSDMB 2002, pp. 7-10. IEEE Computer Society Press, Los Alamitos (2002)
20. Shapiro, B.A., Zhang, K.: Comparing multiple RNA secondary structures using tree comparisons. Comput. Appl. Biosci. 6, 309-318 (1990)
21. Valiente, G.: Algorithms on Trees and Graphs. Springer, Heidelberg (2002)
22. Valiente, G.: A fast algorithmic technique for comparing large phylogenetic trees. In: Consens, M.P., Navarro, G. (eds.) SPIRE 2005. LNCS, vol. 3772, pp. 371-376. Springer, Heidelberg (2005)
23. Woese, C.R., Pace, N.R.: Probing RNA structure, function, and history by comparative analysis. In: Gesteland, R.F., Atkins, J.F. (eds.) The RNA World, pp. 91-117. Cold Spring Harbor Laboratory Press (1993)
24. Zhang, K., Wang, L., Ma, B.: Computing similarity between RNA structures. In: Crochemore, M., Paterson, M.S. (eds.) Combinatorial Pattern Matching. LNCS, vol. 1645, pp. 281-293. Springer, Heidelberg (1999)
25. Hugenholtz, P.: Exploring prokaryotic diversity in the genomic era. Genome Biol. 3, 1-8 (2002)