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RNA pp 67–86Cite as

Web-Based Tools for Studying RNA Structure and Function

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 703))

Abstract

Like protein coding sequences, functional motifs in RNA elements are frequently conserved, but this conservation is most often at the structure level rather than sequence based. Proper characterization of these structural RNA motifs is both the key and the limiting step to understanding the nature of RNA–protein interactions. The discovery of elements targeted by RNA-binding proteins and how they function remains one of the most active, yet elusive areas of RNA biology. Only a limited number of these elements have been well characterized with many of the fundamental rules yet to be discovered. Here we present a comprehensive list of web based resources that can be used in the study and identification of RNA-based structural and regulatory motifs and provide a survey of the informatic resources that can have been developed to facilitate this research.

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References

  1. Griffiths-Jones, S., et al. (2005) Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res 33, suppl_1, D121–D124.

    CAS  PubMed  Google Scholar 

  2. Mignone, F., et al. (2005) UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res 33 Suppl 1, D141–D146.

    Article  CAS  PubMed  Google Scholar 

  3. Huang, H., et al. (2006) RegRNA: an integrated web server for identifying regulatory RNA motifs and elements. Nucleic Acids Res 34, Web Server issue, W429–W434.

    Article  CAS  PubMed  Google Scholar 

  4. Jacobs, G. H., et al. (2006) Transterm–extended search facilities and improved integration with other databases. Nucleic Acids Res 34, Database issue, D37–D40.

    Article  CAS  PubMed  Google Scholar 

  5. Abreu-Goodger, C., et al. (2004) Conserved regulatory motifs in bacteria: riboswitches and beyond. TIGS 20, 475–479.

    CAS  Google Scholar 

  6. Abreu-Goodger, C., Merino, E. (2005) RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements. Nucleic Acids Res 33, Web Server issue, W690–W692.

    Article  CAS  PubMed  Google Scholar 

  7. Pedersen, J. S., et al. (2006) Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol 2, e33.

    Article  CAS  PubMed  Google Scholar 

  8. Torarinsson, E., et al. (2008) Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions. Genome Res 18, 242–251.

    Article  CAS  PubMed  Google Scholar 

  9. Washietl, S., Hofacker, I. L., Stadler, P. F. (2005) Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci 102, 2454–2459.

    Article  CAS  PubMed  Google Scholar 

  10. Berman, H. M., et al. (1992) The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys J 63, 751–759.

    Article  CAS  PubMed  Google Scholar 

  11. Griffiths-Jones, S., et al. (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34, suppl_1, D140–D144.

    Article  CAS  PubMed  Google Scholar 

  12. Bindewald, E., et al. (2008) RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign. Nucleic Acids Res 36, Database issue, D392–D397.

    Article  CAS  PubMed  Google Scholar 

  13. Lestrade, L., Weber, M. J. (2006) snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nucleic Acids Res 34, Database issue, D158–D162.

    Article  CAS  PubMed  Google Scholar 

  14. Xie, J., et al. (2007) Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs. Nucleic Acids Res 35, Database issue, D183–D187.

    Article  CAS  PubMed  Google Scholar 

  15. Rocheleau, L., Pelchat, M. (2006) The Subviral RNA Database: a toolbox for viroids, the hepatitis delta virus and satellite RNAs research. BMC Microbiol 6, 24.

    Article  PubMed  Google Scholar 

  16. Zhou, Y., et al. (2008) GISSD: group I intron sequence and structure database. Nucleic Acids Res 36, Database issue, D31–D37.

    Article  CAS  PubMed  Google Scholar 

  17. Cannone, J. J., et al. (2002) The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3, 2.

    Article  PubMed  Google Scholar 

  18. Eddy, S. R. (2006) Computational analysis of RNAs. Cold Spring Harb Symp Quant Biol 71, 117–128.

    Article  CAS  PubMed  Google Scholar 

  19. Klein, R. J., Eddy, S. R. (2003) RSEARCH: finding homologs of single structured RNA sequences. BMC Bioinformatics 4, 44.

    Article  PubMed  Google Scholar 

  20. Pesole, G., Liuni, S. (1999) Internet resources for the functional analysis of 5′ and 3′ untranslated regions of eukaryotic mRNAs. TIGS 15, 378.

    CAS  Google Scholar 

  21. Dsouza, M., Larsen, N., Overbeek, R. (1997) Searching for patterns in genomic data. Trends Genet 13, 597–498.

    Article  Google Scholar 

  22. Reeder, J., Reeder, J., Giegerich, R. (2007) Locomotif: from graphical motif description to RNA motif search. Bioinformatics 23, i392–i400. data. TIGS, 13, 497–498.

    Article  CAS  PubMed  Google Scholar 

  23. Sakakibara, Y. (2003) Pair hidden Markov models on tree structures. Bioinformatics 19 Suppl 1, i232–i240.

    Article  PubMed  Google Scholar 

  24. Sakakibara, Y., et al. (2007) Stem kernels for RNA sequence analyses. J Bioinformatics Comput Biol 5, 1103–1122.

    Article  CAS  Google Scholar 

  25. Matsui, H., Sato, K., Sakakibara, Y. (2004) Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures, in Proceedings/IEEE Computational Systems Bioinformatics Conference, CSB. IEEE Computational Systems Bioinformatics Conference, pp. 290–299.

    Google Scholar 

  26. Hofacker, I. L. (2003) Vienna RNA secondary structure server. Nucleic Acids Res 31, 3429–3431.

    Article  CAS  PubMed  Google Scholar 

  27. Hofacker, I. L. (2004) RNA secondary structure analysis using the Vienna RNA package. Curr Protoc Bioinformatics (Editoral Board, Andreas D. Baxevanis et al., Chapter 12, Unit 12.2).

  28. Le, S. Y., Zhang, K., Maizel, J. V. (1995) A method for predicting common structures of homologous RNAs. Comput Biomed Res Int J 28, 53–66.

    Article  CAS  Google Scholar 

  29. Macke, T. J., et al. (2001) RNAMotif, an RNA secondary structure definition and search algorithm. Nucleic Acids Res 29, 4724–4735.

    Article  CAS  PubMed  Google Scholar 

  30. Gautheret, D., Lambert, A. (2001) Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles. J Mol Biol 313, 1003–1011.

    Article  CAS  PubMed  Google Scholar 

  31. Lambert, A., et al. (2005) Computing expectation values for RNA motifs using discrete convolutions. BMC Bioinformatics 6, 118.

    Article  PubMed  Google Scholar 

  32. Liu, J., et al. (2005) A method for aligning RNA secondary structures and its application to RNA motif detection. BMC Bioinformatics 6, 89.

    Article  PubMed  Google Scholar 

  33. Xue, C., Liu, G. (2007) RScan: fast searching structural similarities for structured RNAs in large databases. BMC Genomics 8, 257.

    Article  PubMed  Google Scholar 

  34. Busch, A., Backofen, R. (2006) INFO-RNA – a fast approach to inverse RNA folding. Bioinformatic 22, 1823–1831.

    Article  CAS  Google Scholar 

  35. Bafna, V., Zhang, S. (2004) FastR: fast database search tool for non-coding RNA, in Proceedings/IEEE Computational Systems Bioinformatics Conference, CSB. IEEE Computational Systems Bioinformatics Conference, pp. 52–61.

    Google Scholar 

  36. Zhang, S., et al. (2005) Searching genomes for noncoding RNA using FastR. IEEE/ACM Trans Comput Biol Bioinformatics 2, 366–379.

    Article  CAS  Google Scholar 

  37. Thébault, P., et al. (2006) Searching RNA motifs and their intermolecular contacts with constraint networks. Bioinformatics 22, 2074–2080.

    Article  PubMed  Google Scholar 

  38. Veksler-Lublinsky, I., et al. (2007) A structure-based flexible search method for motifs in RNA. J Comput Biol J Comput Mol Cell Biol 14, 908–926.

    CAS  Google Scholar 

  39. Chang, T., et al. (2006) RNAMST: efficient and flexible approach for identifying RNA structural homologs. Nucleic Acids Res 34, Web Server issue, W423–W428.

    Article  CAS  PubMed  Google Scholar 

  40. diBernardo, D, Down, T. and Hubbard, T (2003) ddbRNA: detection of conserved secondary structures in multiple alignments. Bioinformatics 19, 1606–1611.

    Article  CAS  Google Scholar 

  41. Hofacker, I. L. (2007) RNA consensus structure prediction with RNAalifold. Methods Mol Biol 395, 527–544.

    CAS  PubMed  Google Scholar 

  42. Rivas, E., Eddy, S. R. (2001) Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics 2, 8.

    Article  CAS  PubMed  Google Scholar 

  43. Kiryu, H., Kin, T., Asai, K. (2007) Robust prediction of consensus secondary structures using averaged base pairing probability matrices. Bioinformatics 23, 434–441.

    Article  CAS  PubMed  Google Scholar 

  44. Coventry, A., Kleitman, D. J., Berger, B. (2004) MSARI: multiple sequence alignments for statistical detection of RNA secondary structure. Proc Natl Acad Sci 101, 12102–12107.

    Article  CAS  PubMed  Google Scholar 

  45. Knudsen, B., Hein, J. (2003) Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res 31, 3423–3428.

    Article  CAS  PubMed  Google Scholar 

  46. Ruan, J., Stormo, G. D., Zhang, W. (2004) An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots. Bioinformatics 20, 58–66.

    Article  CAS  PubMed  Google Scholar 

  47. Knight, R., Birmingham, A., Yarus, M. (2004) BayesFold: rational 2 degrees folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequences. RNA 10, 1323–1336.

    Article  CAS  PubMed  Google Scholar 

  48. Bindewald, E., Shapiro, B. A. (2006) RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers. RNA 12, 342–352.

    Article  CAS  PubMed  Google Scholar 

  49. Wilm, A., Linnenbrink, K., Steger, G. (2008) ConStruct: Improved construction of RNA consensus structures. BMC Bioinformatics 9, 219.

    Article  PubMed  Google Scholar 

  50. Meyer, I. M., Miklós, I. (2007) SimulFold: simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework. PLoS Comput Biol 3, e149.

    Article  PubMed  Google Scholar 

  51. Dalli, D., et al. (2006) STRAL: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time. Bioinformatics 22, 1593–1599.

    Article  CAS  PubMed  Google Scholar 

  52. Wilm, A., Higgins, D. G., Notredame, C. (2008) R-Coffee: a method for multiple alignment of non-coding RNA. Nucleic Acids Res 36, e52.

    Article  PubMed  Google Scholar 

  53. Moretti, S., et al. (2008) R-Coffee: a web server for accurately aligning noncoding RNA sequences. Nucleic Acids Res 36, Web Server issue, W10–W13.

    Article  CAS  PubMed  Google Scholar 

  54. Steffen, P., et al. (2006) RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics 22, 500–503.

    Article  CAS  PubMed  Google Scholar 

  55. Hamada, M., et al. (2006) Mining frequent stem patterns from unaligned RNA sequences. Bioinformatics 22, 2480–2487.

    Article  CAS  PubMed  Google Scholar 

  56. Tabei, Y., et al. (2008) A fast structural multiple alignment method for long RNA sequences. BMC Bioinformatics 9, 33.

    Article  PubMed  Google Scholar 

  57. Kin, T., Tsuda, K., Asai, K. (2002) Marginalized kernels for RNA sequence data analysis. Genome Inform Int Conf Genome Inform 13, 112–122.

    CAS  Google Scholar 

  58. Le, S., Maizel, J. V., Zhang, K. (2004) An algorithm for detecting homologues of known structured RNAs in genomes, in Proceedings/IEEE Computational Systems Bioinformatics Conference, CSB. IEEE Computational Systems Bioinformatics Conference, pp. 300–310.

    Google Scholar 

  59. Touzet, H. (2007) Comparative analysis of RNA genes: the caRNAc software. Methods Mol Biol 395, 465–474.

    CAS  PubMed  Google Scholar 

  60. Ji, Y., Xu, X., Stormo, G. D. (2004) A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences. Bioinformatics 20, 1591–1602.

    Article  CAS  PubMed  Google Scholar 

  61. Hu, Y. (2003) GPRM: a genetic programming approach to finding common RNA secondary structure elements. Nucleic Acids Res 31, 3446–3449.

    Article  CAS  PubMed  Google Scholar 

  62. Yao, Z., Weinberg, Z., Ruzzo, W. L. (2006) CMfinder–a covariance model based RNA motif finding algorithm. Bioinformatics 22, 445–452.

    Article  CAS  PubMed  Google Scholar 

  63. Pavesi, G., et al. (2004) RNAProfile: an algorithm for finding conserved secondary structure motifs in unaligned RNA sequences. Nucleic Acids Res 32, 3258–3269.

    Article  CAS  PubMed  Google Scholar 

  64. Xu, X., Ji, Y., Stormo, G. D. (2007) RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment. Bioinformatics 23, 1883–1891.

    Article  CAS  PubMed  Google Scholar 

  65. Horesh, Y., et al. (2007) RNAspa: a shortest path approach for comparative prediction of the secondary structure of ncRNA molecules. BMC Bioinformatics 8, 366.

    Article  PubMed  Google Scholar 

  66. Katoh, K., Toh, H. (2008) Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework. BMC Bioinformatics 9, 212.

    Article  PubMed  Google Scholar 

  67. Do, C. B., Foo, C., Batzoglou, S. (2008) A max-margin model for efficient simultaneous alignment and folding of RNA sequences. Bioinformatics 24, i68–i76.

    Article  CAS  PubMed  Google Scholar 

  68. Holmes, I. (2005) Accelerated probabilistic inference of RNA structure evolution. BMC Bioinformatics 6, 73.

    Article  PubMed  Google Scholar 

  69. Lindgreen, S., Gardner, P. P., Krogh, A. (2007) MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing. Bioinformatics 23, 3304–3311.

    Article  CAS  PubMed  Google Scholar 

  70. Kiryu, H., Tabei, Y., et al. (2007) Murlet: a practical multiple alignment tool for structural RNA sequences. Bioinformatics 23, 1588–1598.

    Article  CAS  PubMed  Google Scholar 

  71. Hofacker, I. L., Bernhart, S. H. F., Stadler, P. F. (2004) Alignment of RNA base pairing probability matrices. Bioinformatics 20, 2222–2227.

    Article  CAS  PubMed  Google Scholar 

  72. Will, S., et al. (2007) Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering. PLoS Comput Biol 3, e65.

    Article  PubMed  Google Scholar 

  73. Siebert, S., Backofen, R. (2005) MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons. Bioinformatics 21, 3352–3359.

    Article  CAS  PubMed  Google Scholar 

  74. Anwar, M., Nguyen, T., Turcotte, M. (2006) Identification of consensus RNA secondary structures using suffix arrays. BMC Bioinformatics 7, 244.

    Article  PubMed  Google Scholar 

  75. Bauer, M., Klau, G. W., Reinert, K. (2007) Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization. BMC Bioinformatics 8, 271.

    Article  PubMed  Google Scholar 

  76. Doyle, F., et al. (2008) Bioinformatic tools for studying post-transcriptional gene regulation: the UAlbany TUTR collection and other informatic resources. Methods Mol Biol 419, 39–52.

    Article  CAS  PubMed  Google Scholar 

  77. Gardner, P., Giegerich, R. (2004) A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics 5, 140.

    Article  PubMed  Google Scholar 

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Acknowledgments

We wish to thank the members of the Tenenbaum Lab for helpful suggestions and discussion, especially Chris Zaleski and Frank Doyle. This work was supported in part by NIH grant U01HG004571 to SAT from the NHGRI.

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Authors and Affiliations

  1. Department of Biomedical Sciences, School of Public Health, Gen*NY*Sis Center for Excellence in Cancer Genomics, University at Albany-SUNY, Rensselaer, NY, USA

    Ajish D. George

  2. College of Nanoscale Science and Engineering, Nanoscale Constellation, University at Albany-SUNY, Rensselaer, NY, USA

    Scott A. Tenenbaum

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  1. Ajish D. George
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  2. Scott A. Tenenbaum
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Correspondence to Ajish D. George .

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Editors and Affiliations

  1. The Panum Institute, Dept. of Cellular & Molecular Medicine, University of Copenhagen, Blegdamsvej 3, Copenhagen, 2200N, Denmark

    Henrik Nielsen

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George, A.D., Tenenbaum, S.A. (2011). Web-Based Tools for Studying RNA Structure and Function. In: Nielsen, H. (eds) RNA. Methods in Molecular Biology, vol 703. Humana Press. https://doi.org/10.1007/978-1-59745-248-9_6

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  • DOI: https://doi.org/10.1007/978-1-59745-248-9_6

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-913-0

  • Online ISBN: 978-1-59745-248-9

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