Large scale similarity search for locally stable secondary structures among RNA sequences

IPSJ Transactions on Bioinformatics

Volumn 2, Issue , 2009, Pages 36-46

  Hamada, Michiaki ^a,b,c   Mituyama, Toutai ^b   Asai, Kiyoshi ^b,d  

^a MIZUHO INFORMATION AND RESEARCH INSTITUTE   (Japan)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^c TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

^d UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL APPROACH; COMPUTATIONAL EXPERIMENT; CONSERVED REGIONS; FREE REGION; GENOMIC SEQUENCE; LARGE-SCALE SEQUENCES; NON-CODING RNAS; NOVEL METHODS; RNA SEQUENCES; SCALE SIMILARITY; SEARCH PROBLEM; SECONDARY STRUCTURES;

COMBINATORIAL OPTIMIZATION; NUCLEIC ACIDS; RNA;

PROBLEM SOLVING;

EID: 79954566331     PISSN: None     EISSN: 18826679     Source Type: Journal    
DOI: 10.2197/ipsjtbio.2.36     Document Type: Article

References (35)

1. Abello, J., Resende, M. G. C. and Sudarsky, S.: Massive quasi-clique detection, LATIN'02: Proc. 5th Latin American Symposium on Theoretical Informatics, pp. 598-612, London, UK, Springer-Verlag (2002).
2. Bejerano, G., Pheasant, M., Makunin, I., Stephen, S., Kent, W. J., Mattick, J. S. and Haussler, D.: Ultraconserved elements in the human genome, Science, Vol. 304, No. 5675, pp. 1321-1325 (May 2004). (Pubitemid 38697428)
3. Berezikov, E., Guryev, V., van de Belt, J., Wienholds, E., Plasterk, R. and Cuppen, E.: Phylogenetic shadowing and computational identification of human microRNA genes, Cell, No. 120, pp. 21-24 (Jan. 2005). (Pubitemid 40094599)
4. Carninci, P. and Hayashizaki, Y.: Noncoding RNA transcription beyond annotated genes, Curr. Opin. Genet. Dev., No. 17, pp. 139-144 (Apr. 2007). (Pubitemid 46553830)
5. Costa, F. F.: Non-coding RNAs: New players in eukaryotic biology, Gene, Vol. 357, No. 2, pp. 83-94 (Sep. 2005). (Pubitemid 41297574)
6. Eddy, S. R.: Non-coding RNA genes and the modern RNA world, Nat. Rev. Genet., Vol. 2, No. 12, pp. 919-929 (Dec. 2001). (Pubitemid 33691089)
7. Gardner, P. P. and Giegerich, R.: A comprehensive comparison of comparative RNA structure prediction approaches, BMC Bioinformatics, No. 5, p. 140 (Sep. 2004).
8. Griffiths-Jones, S., Moxon, S., Marshall, M., Khanna, A., Eddy, S. R. and Bateman, A.: Rfam: Annotating non-coding RNAs in complete genomes, Nucleic Acids Res., 33 (Database issue), pp. 121-124 (Jan 2005).
9. Hamada, M., Kiryu, H., Sato, K., Mituyama, T. and Asai, K.: Prediction of RNA secondary structure using generalized centroid estimators, Bioinformatics Advance Access published on December 18 (2008).
10. Hamada, M., Tsuda, K., Kudo, T., Kin, T. and Asai, K.: Mining frequent stem patterns from unaligned RNA sequences, Bioinformatics, No. 22, pp. 2480-2487 (Oct. 2006). (Pubitemid 44560754)
11. Hōchsmann, M., Tōller, T., Giegerich, R. and Kurtz, S.: Local similarity in rna secondary structures, CSB'03: Proc. IEEE Computer Society Conference on Bioinformatics, p. 159, Washington, DC, USA, IEEE Computer Society (2003).
12. Höchsmann, M., Voss, B. and Giegerich, R.: Pure multiple rna secondary structure alignments: A progressive profile approach, IEEE/ACM Trans. Comput. Biology Bioinform., Vol. 1, No. 1, pp. 53-62 (2004).
13. Hofacker, I. L., Fekete, M. and Stadler, P. F.: Secondary structure prediction for aligned RNA sequences, J. Mol. Biol., Vol. 319, No. 5, pp. 1059-1066 (June 2002). (Pubitemid 34729418)
14. Hofacker, I. L., Priwitzer, B. and Stadler, P. F.: Prediction of locally stable RNA secondary structures for genome-wide surveys, Bioinformatics, Vol. 20, No. 2, pp. 186-190 (Jan. 2004). (Pubitemid 38195676)
15. Huttenhofer, A., Schattner, P. and Polacek, N.: Non-coding RNAs: hope or hype?, Trends Genet., Vol. 21, No. 5, pp. 289-297 (May 2005). (Pubitemid 40558935)
16. Kapranov, P., Cheng, J., Dike, S., Nix, D. A., Duttagupta, R., Willingham, A. T., Stadler, P. F., Hertel, J., Hackermuller, J., Hofacker, I. L., Bell, I., Cheung, E., Drenkow, J., Dumais, E., Patel, S., Helt, G., Ganesh, M., Ghosh, S., Piccolboni, A., Sementchenko, V., Tammana, H. and Gingeras, T. R.: RNA maps reveal new RNA classes and a possible function for pervasive transcription, Science, Vol. 316, No. 5830, pp. 1484-1488 (June 2007). (Pubitemid 46906616)
17. Kin, T., Yamada, K., Terai, G., Okida, H., Yoshinari, Y., Ono, Y., Kojima, A., Kimura, Y., Komori, T. and Asai, K.: fRNAdb: A platform for mining/annotating functional RNA candidates from non-coding RNA sequences, Nucleic Acids Res., No. 35 (Database issue), pp. 145-148 (Jan. 2007).
18. Kiryu, H., Kin, T. and Asai, K.: Rfold: An exact algorithm for computing local base pairing probabilities, Bioinformatics, No. 24, pp. 367-373 (Feb. 2008). (Pubitemid 351189012)
19. Klein, R. J. and Eddy, S. R.: RSEARCH: Finding homologs of single structured RNA sequences, BMC Bioinformatics, No. 4, p. 44 (Sep. 2003).
20. Lunter, G., Ponting, C. P. and Hein, J.: Genome-wide identification of human functional DNA using a neutral indel model, PLoS Comput. Biol., Vol. 2, No. 1, e5 (Jan. 2006).
21. Matera, A. G., Terns, R. M. and Terns, M. P.: Non-coding RNAs: Lessons from the small nuclear and small nucleolar RNAs, Nat. Rev. Mol. Cell. Biol., Vol. 8, No. 3, pp. 209-220 (Mar. 2007).
22. Mattick, J. S. and Makunin, I. V.: Non-coding RNA, Hum. Mol. Genet., 15 Spec No. 1, pp. 17-29 (Apr. 2006).
23. Mituyama, T., Yamada, K., Hattori, E., Okida, H., Ono, Y., Terai, G., Yoshizawa, A., Komori, T. and Asai, K.: The Functional RNA Database 3.0: Databases to support mining and annotation of functional RNAs, Nucleic Acids Res. (Oct. 2008).
24. Nakaya, H. I., Amaral, P. P., Louro, R., Lopes, A., Fachel, A. A., Moreira, Y. B., El-Jundi, T. A., da Silva, A. M., Reis, E. M. and Verjovski-Almeida, S.: Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissuespecific patterns and enrichment in genes related to regulation of transcription, Genome Biol., Vol. 8, No. 3, R43 (2007).
25. Okada, Y., Fujibuchi, W. and Horton, P.: A biclustering method for gene expression module discovery using closed itemset enumeration algorithm, IPSJ Transactions on Bioinformatics, No. 48 (SIG5), pp. 39-48 (2007).
26. Pedersen, J. S., Bejerano, G., Siepel, A., Rosenbloom, K., Lindblad-Toh, K., Lander, E. S., Kent, J., Miller, W. and Haussler, D.: Identification and classification of conserved RNA secondary structures in the human genome, PLoS Comput. Biol., Vol. 2, No. 4, e33 (Apr. 2006).
27. Pitsoulis, L. and Resende, M.: Greedy randomized adaptive search procedures, Pardalos, P. and Resende, M. (Eds.), Handbook of Applied Optimization, pp. 168-183. Oxford University Press (2002).
28. Large Scale Similarity Search for Locally Stable Secondary Structures
29. Pollard, K. S., Salama, S. R., Lambert, N., Lambot, M.-A., Coppens, S., Pedersen, J. S., Katzman, S., King, B., Onodera, C., Siepel, A., Kern, A. D., Dehay, C., Igel, H., Ares, M. J., Vanderhaeghen, P. and Haussler, D.: An RNA gene expressed during cortical development evolved rapidly in humans, Nature, Vol. 443, No. 7108, pp. 167-172 (Sep. 2006). (Pubitemid 44387600)
30. Simons, C., Pheasant, M., Makunin, I. V. and Mattick, J. S.: Transposon-free regions in mammalian genomes, Genome Res., Vol. 16, No. 2, pp. 164-172 (Feb. 2006). (Pubitemid 43200264)
31. Torarinsson, E., Sawera, M., Havgaard, J. H., Fredholm, M. and Gorodkin, J.: Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure, Genome Res., Vol. 16, No. 7, pp. 885-889 (July 2006). (Pubitemid 43992912)
32. Washietl, S., Hofacker, I. L., Lukasser, M., Huttenhofer, A. and Stadler, P. F.: Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome, Nat. Biotechnol., Vol. 23, No. 11, pp. 1383-1390 (Nov. 2005). (Pubitemid 41679390)
33. Washietl, S., Hofacker, I. L. and Stadler, P. F.: Fast and reliable prediction of noncoding RNAs, Proc. Natl. Acad. Sci. USA, Vol. 102, No. 7, pp. 2454-2459 (Feb. 2005). (Pubitemid 40279397)
34. Will, S., Reiche, K., Hofacker, I., Stadler, P. and Backofen, R.: Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering, PLoS Comput. Biol., No. 3, e65 (Apr. 2007).
35. Zhang, Z., Pang, A. W. C. and Gerstein, M.: Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human, BMC Evol. Biol., No. 7 (Suppl) 1, S14 (2007).