Structural alignment of pseudoknotted RNA

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

Volumn 3909 LNBI, Issue , 2006, Pages 143-158

  Dost, Banu ^a   Han, Buhm ^a   Zhang, Shaojie ^a   Bafna, Vineet ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; COMPUTATION THEORY; GENES; RNA; VIRUSES;

EUKARYOTIC PSEUDOKNOTS; MOUSE GENOME; PSEUDOKNOTTED RNA; TARGET ALIGNED SEQUENCE; VIRAL GENOME;

MOLECULAR BIOLOGY;

EID: 33745804035     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/11732990_13     Document Type: Conference Paper

References (31)

1. Argaman, L., et al.: Novel small RNA-encoding genes in the intergenic regions of Escherischia coli. Curr. Biol. 11 (2001) 941-950
2. Novina, C.D., Sharp, P.A.: The RNAi revolution. Nature 430 (2004) 161-164 News.
3. Storz, G.: An expanding universe of noncoding RNAs. Science 296 (2002) 1260-1263
4. Vitreschak, A., Rodionov, D., Mironov, A., Gelfand, M.: Riboswitches: the oldest mechanism for the regulation of gene expression? Trends in Genetics 20 (2003) 44-50
5. Winkler, W.C., Breaker, R.R.: Genetic control by metabolite-binding riboswitches. Chem-biochem 4 (2003) 1024-1032
6. Eddy, S.: Non-coding RNA genes and the modern RNA world. Nature Reviews in Genetics 2 (2001) 919-929
7. Jaeger, J., Turner, D., Zuker, M.: Improved prediction of secondary structures for RNA. Proceedings of the National Academy of Sciences 86 (1989) 7706-7710
8. Zuker, M., Sankoff, D.: RNA secondary structures and their prediction. Bull. Math. Biol. 46 (1984) 591-621
9. Rivas, E., Eddy, S.: Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs. Bioinformatics 16 (2000) 583-605
10. Griffiths-Jones, S., Moxon, S., Marshall, M., Khanna, A., Eddy, S.R., Bateman, A.: Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res 33 (2005) 121-124
11. Klein, R., Eddy, S.: Rsearch: Finding homologs of single structured rna sequences. BMC Bioinformatics 4 (2003) 44
12. Rastogi, T., Beattie, TL., Olive, J.E., Collins, R.A.: A long-range pseudoknot is required for activity of the Neurospora VS ribozyme. EMBO J 15 (1996) 2820-2825
13. Adams, P.L., Stahley, M.R., Kosek, A.B., Wang, J., Strobel, S.A.: Crystal structure of a self-splicing group I intron with both exons. Nature 430 (2004) 45-50
14. Theimer, C.A., Blois, C.A., Feigon, J.: Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function. Mol Cell 17 (2005) 671-682
15. Nixon, P.L., Rangan, A., Kim, Y.G., Rich, A., Hoffman, D.W., Hennig, M., Giedroc, D.P: Solution structure of a luteoviral P1-P2 frameshifting mRNA pseudoknot. J Mol Biol 322 (2002) 621-633
16. Akutsu, T: Dynamic programming algorithm for RNA secondary structure prediction with pseudoknots. Disc. Appl. Math. 104 (2000) 45-62
17. Dirks, R.M., Pierce, N.A.: A partition function algorithm for nucleic acid secondary structure including pseudoknots. J Comput Chem 24 (2003) 1664-1677
18. Evans, P.: Algorithms and Complexity for Annotated Sequence Analysis. PhD thesis, University of Victoria, Victoria BC, Canada (1964)
19. Jiang, T., Lin, G., Ma, B., Zhang, K.: A general edit distance between rna structures. Journal of Computational Biology 9 (2002) 371-388
20. Rivas, E., Eddy, S.: A Dynamic Programming Algorithm for RNA Structure Prediction Including Pseudoknots. Journal of Molecular Biology 285 (1999) 2053-2068
21. Condon, A., Davy, B., Rastegari, B., Tarrant, F., Zhao, S.: Classifying RNA Pseudoknotted Structures. Theoretical Computer Science 320 (2004) 35-50
22. Rastegari, B., Condon, A.: Linear time algorithm for parsing rna secondary structure. In: 5th Workshop on Algorithms in Bioinformatics (WABI). (2005)
23. Matsui, H., Sato, K., Sakakibara, Y.: Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures. Bioinformatics 21 (2005) 2611-2617
24. Bafna, V., Muthukrishnan, S., Ravi, R.; Computing similarity between RNA strings. Combinatorial Pattern Matching 937 (1995) 1-14
25. Durbin, R., Eddy, S., Krogh, A., Mitchison, G.: 10.3 Covariance models: SCFG-based RNA profiles. In: Biological Sequence Analysis. Cambridge University Press (1998)
26. Zhang, S., Mass, B., Eskin, E., Bafna, V.: Searching genomes for non-coding rna using fastr. IEEE Transactions on Computational Biology and Bioinformatics 2 (200) 366-379
27. Weinberg, Z., Ruzzo, W.L.: Faster genome annotation of non-coding rna families without loss of accuracy. In: Proceedings of the Annual Intl. Conference on Computational Biology (RECOMB). (2004)
28. Zhang, S., Borovok, I., Aharonowitz, Y., Sharan, R., Bafna, V.: A Sequence-Based Filtering Method for ncRNA Identification and its Application to Searching for Riboswitch Elements. Manuscript (2005)
29. Baranov, P.V., Henderson, C.M., Anderson, C.B., Gesteland, R.F., Atkins, J.F., Howard, M.T.: Programmed ribosomal frameshifting in decoding the SARS-CoV genome. Virology 332 (2005) 498-510
30. Williams, G.D., Chang, R.Y., Brian, D.A.: A phylogenetically conserved hairpin-type 3' untranslated region pseudoknot functions in coronavirus RNA replication. J Virol 73 (1999) 8349-8355
31. Ben-Asouli, Y., Banai, Y., Pel-Or, Y., Shir, A., Kaempfer, R.: Human interferon-gamma mRNA autoregulates its translation through a pseudoknot that activates the interferon-inducible protein kinase PKR. Cell 108 (2002) 221-232