Tree decomposition based fast search of RNA structures including pseudoknots in genomes

Proceedings - 2005 IEEE Computational Systems Bioinformatics Conference, CSB 2005

Volumn 2005, Issue , 2005, Pages 223-234

  Song, Yinglei ^a   Malmberg, Russell ^b   Liu, Chunmei ^a   Pan, Fangfang ^b   Cai, Liming ^a,b  

^a University of Georgia ^*  (United States)

^b UNIVERSITY OF GEORGIA   (United States)

Author keywords

Covariance model; Pseudoknot search; RNA secondary structure profiling; Tree decomposition

Indexed keywords

ALGORITHMS; COMPUTATION THEORY; COMPUTATIONAL METHODS; COMPUTER PROGRAMMING; GENETIC ENGINEERING; GRAPH THEORY; MATHEMATICAL MODELS; RNA;

COVARIANCE MODEL; PSEUDOKNOT SEARCH; RNA SECONDARY STRUCTURE PROFILING; TREE DECOMPOSITION;

TREES (MATHEMATICS);

ALGORITHM; ARTICLE; CHEMICAL MODEL; CHROMOSOME MAP; COMPUTER SIMULATION; CONFORMATION; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

ALGORITHMS; BASE SEQUENCE; CHROMOSOME MAPPING; COMPUTER SIMULATION; MODELS, CHEMICAL; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EID: 33745492418     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/csb.2005.52     Document Type: Conference Paper

References (27)

1. S. Amborg and A. Proskurowski. Linear time algorithms for np-hard problems restricted to partial k-trees. Discrete Applied Mathematics, 23:11-24, 1989.
2. V. Bafna and S. Zhang. Fastr: Fast database search tool for non-coding ma. Proceedings of the 3rd IEEE Computational Systems Bioinformatics Conference, pages 52-61, 2004.
3. H. L. Bodlaender. Classes of graphs with bounded tree-width. Tech. Rep. RUU-CS-86-22, University of Utrecht, 1986.
4. M. Brown and C. Wilson. Rna pseudoknot modeling using intersections of stochastic context free grammars with applications to database search. Proceedings of Pacific Symposium on Biocomputing, pages 109-125, 1995.
5. L. Cai, R. Malmberg, and Y. Wu. Stochastic modeling of pseudoknot structures: A grammatical approach. Bioinformatics, 19:i66-i73, 2003.
6. A. T. Dandjinou, N. Ĺvesque, S. Larose, J. Lucier, S. A. Elela, and R. J. Wellinger. A phylogenetically based secondary structure for the yeast telomerase ma. Current Biology, 14:1148-1158, 2004.
7. R. Durbin, S. Eddy, A. Krogh, and G. Mitchison. Biological sequence analysis: Probabilistic models of proteins and nucleic acids. Cambridge Univ. Press, The EdinburghBuilding, Cambridge CB2 2RU, UK, 1998.
8. S. Eddy and R. Durbin. Rna sequence analysis using covariance models. Nucleic Acids Research, 22:2079-2088, 1994.
9. D. Eppstein. Subgraph isomorphism in planar graphs and related problems. Journal of Graph Algorithms and Applications, 3.3:1-27, 1999.
10. D. N. Frank and N. R. Pace. Ribonuclease p: unity and diversity in a trna processing ribozyme. Annu Rev Biochem, 67:153-180, 1998.
11. D. Gautheret and A. Lambert. Direct ma motif definition and identification from multiple sequence alignments using secondary structure profiles. Journal of Molecular Biology, 313:1003-1011, 2001.
12. S. J. Geobel, B. Hsue, T. F. Dombrowski, and P. S. Masters. Characterizationof the ma components of a putative molecular switch in the 3' untranslated region of the murine coronavirus genome. Journal of Virology, 78:669-682, 2004.
13. S. Griffiths-Jones, A. Bateman, M. Marshall, A. Khanna, and S. R. Eddy. Rfam: an ma family database. Nucleic Acids Research, 31:439-441, 2003.
14. R. J. Klein and S. R. Eddy. Rsearch: Finding homologs of single structured ma sequences. BMC Bioinfonnatics, 4:44, 2003.
15. C. Liu, Y. Song, R. Malmberg, and L. Cai. Profiling and searching for ma pseudoknot structures in genomes. Proceedings cf 2005 International Workshop in Bioinfonnatics Research and Applications, to appear, 2005.
16. T. M. Lowe and S. R. Eddy, tmascan-se: A program for improved detection of transferma genes in genomic sequence. Nucleic Acids Research, 25:955-964, 1997.
17. J. Matousek and R. Thomas. On the complexity of finding iso- and other morphisms for partial k-trees. Discrete Mathematics, 108:343-364, 1992.
18. N. Nameki, B. Felden, J. F. Atkins, R. F. Gesteland, H. Himeno, and A. Muto. Functional and structural analysis of a pseudoknot upstream of the tag-encoded sequence in e. coli tmma. Journal of Molecular Biology, 286(3):733-744, 1999.
19. V. T. Nguyen, T. Kiss, A. A. Michels, and O. Bensaude. 7sk small nuclear ma binds to and inhibits the activity of cdk9/cyclin t complexes. Nature, 414:322-325, 2001.
20. E. Rivas and S. Eddy. The language of ma: a formal grammar that includes pseudoknots. Bioinfomatics, 16:334-340, 2000.
21. E. Rivas and S. R. Eddy. A dynamic programming algorithm for ma structure prediction including pseudoknots. Journal of Molecular Biology, 285:2053-2068, 1999.
22. E. Rivas and S. R. Eddy. Noncoding ma gene detection using comparative sequence analysis. BMC Bioinformatics, 2:8, 2001.
23. E. Rivas, R. J. Klein, T. A. Jones, and S. R. Eddy. Computational identification of noncoding mas in e. coli by comparative genomics. Current Biology, 11:1369-1373, 2001.
24. N. Robertson and P. D. Seymour. Graph minors ii. algorithmic aspects of tree-width. Journal of Algorithms, 7:309-322, 1986.
25. Y. Uemura, A. Hasegawa, Y. Kobayashi, and T. Yokomori. Tree adjoining grammars for ma structure prediction. Theoretical Computer Science, 210:277-303, 1999.
26. Z. Weinberg and W. L. Ruzzo. Faster genome annotation of non-coding ma families without loss of accuracy. Proceedings the Eighth Annual International Conference on Computational Molecular Biology, pages 243-25 1,2004.
27. Z. Yang, Q. Zhu, K. Luo, and Q. Zhou. The 7sk small nuclear ma inhibits the cdk9/cyclin t1 kinase to control transcription. Nature, 414:317-322, 2001.