Automated motif extraction and classification in RNA tertiary structures

RNA

Volumn 14, Issue 12, 2008, Pages 2489-2497

  Djelloul, Mahassine ^a   Denise, Alain ^a,b  

^a UFR 919 Laboratoire d'Informatique Pour la Mécanique et les Sciences de l'Ingénieur   (France)

^b UNIVERSITÉ PARIS SACLAY   (France)

Author keywords

Clustering; Graph similarity; RNA tertiary structure

Indexed keywords

BACTERIAL RNA; RNA 16S;

ARTICLE; CRYSTAL STRUCTURE; ESCHERICHIA COLI; HALOARCULA MARISMORTUI; NONHUMAN; PRIORITY JOURNAL; RNA EXTRACTION; RNA STRUCTURE; THERMUS THERMOPHILUS;

ESCHERICHIA COLI; HALOARCULA MARISMORTUI; THERMUS THERMOPHILUS;

EID: 57049101474     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.1061108     Document Type: Article

References (36)

1. Artymiuk, P.J., Spriggs, R.V., and Willett, P. 2005. Graph theoretic methods for the analysis of structural relationships in biological macromolecules: Research articles. J. Am. Soc. Inf. Sci. Technol. 56: 518-528.
2. Batey, R.T., Rambo, R.P., and Doudna, J.A. 1999. Tertiary motifs in RNA structure and folding. Angew. Chem. Int. Ed. 32: 2326-2343.
3. Berman, H.M., Olson, W.K., Beveridge, D.L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S.-H., Srinivasan, A.R., and Schneider, B. 1992. The nucleic acid database: A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J. 63: 751-759.
4. Bindewald, E., Hayes, R., Yingling, Y.G., Kasprzak, W., and Shapiro, B.A. 2008. RNAJunction: A database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign. Nucleic Acids Res. 36: 392-397.
5. Corell, C.C., Beneken, J., Plantinga, M.J., Lubbers, M., and Chan, Y.-L. 2003. The common and the distinctive features of the bulged-G motif based on a 1.04 Å resolution RNA structure. Nucleic Acids Res. 31: 6806-6818.
6. Duarte, C.M., Wadley, L.M., and Pyle, A.M. 2003. RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space. Nucleic Acids Res. 31: 4755-4761.
7. Garey, M.R. and Johnson, D.S. 1979. Computers and intractability: A guide to the theory of NP Completeness. Freeman, New York.
8. Harrison, A., South, D.R., Willett, P., and Artymiuk, P.J. 2003. Representation, searching and discovery of patterns of bases in complex RNA structures. J. Comput. Aided Mol. Des. 17: 537-549.
9. Hendrix, D.K., Brenner, S.E., and Holbrook, S.R. 2005. RNA structural motifs: Building blocks of a modular molecule. Q. Rev. Biophys. 38: 221-243.
10. Hershkovitz, E., Tannenbaum, E., Howerton, S.B., Sheth, A., Tannenbaum, A., and Williams, L.D. 2003. Automated identification of RNA conformational motifs: Theory and application to the HM LSU 23S rRNA. Nucleic Acids Res. 31: 6249-6257.
11. Holbrook, S.R. 2005. RNA structure: The long and the short of it. Curr. Opin. Struct. Biol. 15: 302-308.
12. Huang, H.C., Nagaswamy, U., and Fox, G.E. 2005. The application of cluster analysis in the intercomparison of loop structures in RNA. RNA 11: 412-423.
13. Jossinet, F. and Westhof, E. 2005. Sequence to Structure (S2S): Display, manipulate and interconnect RNA data from sequence to structure. Bioinformatics 21: 3320-3321.
14. Le, S.Q., Ho, T.B., and Phan, T.T.H. 2004. A novel graph-based similarity measure for 2D chemical structures. Genome Inform. 15: 82-91.
15. Lemieux, S. and Major, F. 2002. RNA canonical and noncanonical base-pairing types: A recognition method and complete repertoire. Nucleic Acids Res. 30: 4250-4263.
16. Leontis, N.B. and Westhof, E. 2001. Geometric nomenclature and classification of RNA base pairs. RNA 7: 499-512.
17. Leontis, N.B. and Westhof, E. 2003. Analysis of RNA motifs. Curr. Opin. Struct. Biol. 13: 300-308.
18. Leontis, N.B., Stombaugh, J., and Westhof, E. 2002a. Motif prediction in ribosomal RNAs. Lessons and prospects for automated motif prediction in homologous RNA molecules. Biochimie 84: 961-973.
19. Leontis, N.B., Stombaugh, J., and Westhof, E. 2002b. Survey and summary. The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res. 30: 3497-3531.
20. Leontis, N.B., Lescoute, A., and Westhof, E. 2006. The building blocks and motifs of RNA architecture. Curr. Opin. Struct. Biol. 16: 1-9.
21. Lescoute, A. and Westhof, E. 2006a. The A-minor motifs in the decoding recognition process. Biochimie 88: 993-999.
22. Lescoute, A. and Westhof, E. 2006b. Topology of three-way junctions in folded RNAs. RNA 12: 83-93.
23. Lescoute, A., Leontis, N.B., Massire, C., and Westhof, E. 2005. Recurrent structural RNA motifs, isostericity matrices and sequence alignments. Nucleic Acids Res. 33: 2395-2409.
24. Moore, P.B. 1999. Structural motifs in RNA. Annu. Rev. Biochem. 68: 287-300.
25. Nissen, P., Ippolito, J.A., Ban, N., Moore, P.B., and Steitz, T.A. 2001. RNA tertiary interactions in the large ribosomal subunit: The Aminor motif. Proc. Natl. Acad. Sci. 98: 4899-4903.
26. Oranit, D., Nussinov, R., and Wolfson, H. 2005. ARTS: Alignment of RNA tertiary structures. Bioinformatics 21: ii47-ii53.
27. Ponty, Y. 2006. Modélisation de séquences génomiques structurées, génération aléatoire et application. Ph.D. thesis, Université Paris-Sud 11.
28. Sarver, M., Zirbel, C.L., Stombaugh, J., Mokdad, A., and Leontis, N.B. 2008. FR3D: Finding local and composite recurrent structural motifs in RNA 3D structures. J. Math. Biol. 56: 215-252.
29. Shapiro, B.A. 1988. An algorithm for comparing multiple RNA secondary structures. Comput. Appl. Biosci. 4: 387-393.
30. Smit, S., Rother, K., Heringa, J., and Knight, R. 2008. From knotted to nested RNA structures: A variety of computational methods for pseudoknot removal. RNA 14: 410-416.
31. Szep, S., Wang, J., and Moore, P.B. 2003. The crystal structure of a 26-nucleotide RNA containing a hook-turn. RNA 9: 44-51.
32. Valiente, G. 2002. Algorithms on trees and graphs. Springer, Berlin.
33. Wadley, L.M. and Pyle, A.M. 2004. The identification of novel RNA structural motifs using COMPADRES: An automated approach to structural discovery. Nucleic Acids Res. 32: 6650-6659.
34. Westhof, E. and Auffinger, P. 2000. RNA tertiary structure. In Encyclopedia of analytical chemistry (ed. R.A. Meyers), pp. 5222-5232. J. Wiley, Chichester, UK.
35. Yang, H., Jossinet, F., Leontis, N., Chen, L., Westbrook, J., Berman, H.M., and Westhof, E. 2003. Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res. 31: 3450-3460.
36. Zuker, M. and Sankoff, D. 1984. RNA secondary structures and their prediction. Bull. Math. Biol. 46: 591-621.