Interval-based distance function for identifying RNA structure candidates

Journal of Theoretical Biology

Volumn 269, Issue 1, 2011, Pages 280-286

  Chen, Qingfeng ^a,b   Li, Gang ^c   Phoebe Chen, Yi Ping ^b  

^a GUANGXI UNIVERSITY   (China)

^b LA TROBE UNIVERSITY   (Australia)

^c DEAKIN UNIVERSITY   (Australia)

Author keywords

Clustering; Distance; Interval; RNA; Secondary structure

Indexed keywords

ALGORITHM; CLUSTER ANALYSIS; DATA SET; GENETIC STRUCTURE; IDENTIFICATION METHOD; RNA;

ALGORITHM; ARTICLE; CLUSTER ANALYSIS; INTERVAL BASED DISTANCE FUNCTION; NUCLEIC ACID DATABASE; PRIORITY JOURNAL; RNA STRUCTURE; STRUCTURAL HOMOLOGY; STRUCTURE ANALYSIS;

COMPUTATIONAL BIOLOGY; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RNA;

EID: 78249281653     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2010.11.002     Document Type: Article

References (25)

1. Agrawal, R., Imielinski, T., Swami, A., 1993. Mining association rules between sets of items in large databases. In: Proceedings of the ACM SIGMOD Conference on Management of Data, pp. 207-216.
2. Arkhangel'skii A.V., Pontryagin L.S. General topology I: basic concepts and constructions dimension theory. Encyclopedia of Mathematical Sciences 1990, Springer.
3. Chan, K., Fu, W., 1999. Efficient time series matching by wavelets. In: Proceedings of the 15th IEEE International Conference on Data Engineering, pp. 126-133.
4. Ester, M., Kriegel, H.P, Sander, J., Xu, X., 1996. A density-based algorithm for discovering clusters in large spatial databases with noise. In: Proceedings of the Second International Conference on Knowledge Discovery and Data Mining, AAAI Press, pp. 226-231.
5. Faloutsos C., Barber R., Flickner M., Hafner J., Niblack W., Petkovic D., Equitz W. Efficient and effective querying by image content. Journal of Intelligent Information Systems 1994, 3(3-4):231-262.
6. Francois, D., Christian, H., Kay, J.W., 2008. A growth model for RNA secondary structures. Journal of Statistical Mechanics: Theory and Experiment, 04008.
7. Gardner P.P., Daub J., Tate J.G., Nawrocki E.P., Kolbe D.L., Lindgreen S., Wilkinson A.C., Finn R.D., Griffiths-Jones S., Eddy S.R., Bateman A. Rfam: updates to the RNA families database. Nucleic Acids Research 2009, 37:136-140.
8. Han J.W., Kamber M. Data Mining: Concepts and Techniques 2006, Morgan Kaufmann Publishers. second ed.
9. Heyer L.J., Kruglyak S., Yooseph S. Exploring expression data: identification and analysis of coexpressed genes. Genome Research 1999, 9:1106-1115.
10. http://toolkit.tuebingen.mpg.de/blastclust.
11. Janssen S., Reeder J., Giegerich R. Shape based indexing for faster search of RNA family databases. BMC Bioinformatics 2008, 9:131.
12. Lawrence, H. (Ed.), 1993. Artificial Intelligence and Molecular Biology. MIT Press.
13. Lu Y., Lu S.Y., Fotouhi F., Deng Y.P., Brown S. Incremental genetic K-means algorithm and its application in gene expression data analysis. BMC Bioinformatics 2004, 5:172.
14. Mattick J.S. RNA regulation: a new genetics. Nature Reviews Genetics 2004, 5(4):316-323.
15. Napthine S., Liphardt J., Bloys A., Routledge S., Brierley I. The role of RNA pseidoknot stem 1 length in the promotion of efficient-1 ribosomal frameshifting. Journal of Molecular Biology 1999, 288:305-320.
16. Ng, R.T., Han, J., 1994. Efficient and effective clustering methods for spatial data mining. In: Proceedings of the 20th VLDB Conference, pp. 144-155.
17. Pang K.C., Stephen S., Dinger M.E., Engström P.G., Lenhard B., Mattick J.S. RNAdb 2.0-an expanded database of mammalian non-coding RNAs. Nucleic Acids Research 2007, 35:D178-D182.
18. Panchenko A.R., Madej T. Structural similarity of loops in protein families: toward the understanding of protein evolution. BMC Evolutionary Biology 2005, 5(1):10.
19. Searls D.B. The language of genes. Nature 2002, 420:211-217.
20. van Batenburg F.H., Gultyaev A.P., Pleij C.W. PseudoBase: structural information on RNA pseudoknots. Nucleic Acids Research 2001, 29(1):194-195.
21. van Batenburg F.H., Gultyaev A.P., Pleij C.W., Ng J., Iliehoek J. PseudoBase: a database with RNA pseudoknots. Nucleic Acids Research 2000, 28(1):201-204.
22. Xu X., Ji Y., Stormo G.D. RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment. Bioinformatics 2007, 23(15):1883-1891.
23. Zakai M. General distance criteria. IEEE Transactions on Information Theory 1964, 10(1):94-95.
24. Zhang S.J., Haas B., Eskin E., Bafna V. Searching genomes for noncoding RNA using FastR. IEEE/ACM Transaction on Computational Biology and Bioinformatics 2005, 2(4):366-379.
25. Zhang, T., Ramakrishnan, R., Livny, M., 1996. BIRCH: An efficient data clustering method for very large databases. In: Proceedings of ACM SIGMOD Conference, pp. 103-114.