Covariant evolutionary event analysis for base interaction prediction using a relational database management system for RNA

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

Volumn 5566 LNCS, Issue , 2009, Pages 200-216

  Xu, Weijia ^a   Ozer, Stuart ^b   Gutell, Robin R ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b NONE   (United States)

Author keywords

Bioinformatics; Biological database; RNA; Sequence Analysis

Indexed keywords

16S RIBOSOMAL RNA; BASE PAIR INTERACTIONS; BASE PAIRING; BASE STACKING; BIOLOGICAL DATABASE; COMMON STRUCTURES; COMPARATIVE SEQUENCE ANALYSIS; COVARIATION; EVOLUTIONARY EVENTS; EVOLUTIONARY RELATIONSHIPS; INTERACTION PREDICTION; MICROSOFT SQL SERVER; NEW APPROACHES; PHYLOGENETIC CLASSIFICATIONS; RELATIONAL DATABASE; RELATIONAL DATABASE MANAGEMENT SYSTEMS; RNA STRUCTURES; SECONDARY STRUCTURES; SEQUENCE ANALYSIS; STRUCTURAL ELEMENTS;

BIOINFORMATICS; MANAGEMENT INFORMATION SYSTEMS; NUCLEIC ACIDS; RNA;

DATABASE SYSTEMS;

EID: 69049115490     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-02279-1_15     Document Type: Conference Paper

References (39)

1. Cannone, J.J., et al.: The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3(1), 2 (2002)
2. Gutell, R.R., et al.: Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods. Nucleic Acids Res. 20(21), 5785-5795 (1992)
3. Gutell, R.R., et al.: Comparative anatomy of 16-S-like ribosomal RNA. Prog. Nucleic Acid Res. Mol. Biol. 32, 155-216 (1985)
4. Gutell, R.R., Noller, H.F., Woese, C.R.: Higher order structure in ribosomal RNA. EMBO J. 5(5), 1111-1113 (1986)
5. Woese, C.R., Winker, S., Gutell, R.R.: Architecture of ribosomal RNA: constraints on the sequence of tetra-loops. Proceedings of the National Academy of Sciences of the United States of America 87(21), 8467-8471 (1990)
6. Benson, D.A., et al.: GenBank. Nucleic acids research, 35(Database issue), pp. D21-D25 (2007)
7. Walker, E.: A Distributed File System for a Wide-area High Performance Computing Infrastructure. In: Proceedings of the 3rd conference on USENIX Workshop on Real, Large Distributed Systems, vol. 3. USENIX Association, Seattle (2006)
8. Macke, T.J.: The Ae2 Alignment Editor (1992)
9. Walker, E.: Creating Private Network Overlays for High Performance Scientific Computing. In: ACM/IFIP/USENIX International Middleware Conference. ACM, Newport Beach (2007)
10. Stephens, S.M., et al.: Oracle Database 10g: a platform for BLAST search and Regular Expression pattern matching in life sciences. Nucl. Acids Res. 33, 675-679 (2005)
11. Eckman, B.: Efficient Access to BLAST using IBM DB2 Information Integrator. IBM health care & life sciences (September 2004)
12. Tata, S., Patel, J.M.: PiQA: an algebra for querying protein data sets. In: Proceedings of 15th International Conference on Scientific and Statistical Database Management, pp. 141-150 (2003)
13. Miranker, D.P., Xu, W., Mao, R.: MoBIoS: a Metric-Space DBMS to Support Biological Discovery. In: 15th International Conference on Scientific and Statistical Database Management (SSDBM 2003), Cambridge, Massachusetts, USA. IEEE Computer Society, Los Alamitos (2003)
14. Xu, W., et al.: Using MoBIoS' Scalable Genome Joins to Find Conserved Primer Pair Candidates Between Two Genomes. Bioinformatics 20, i371-i378 (2004)
15. Xu, W., et al.: On integrating peptide sequence analysis and relational distance-based indexing. In: IEEE 6th Symposium on Bioinformatics and Bioengineering (BIBE 2006), Arlington, VA, USA (accepted) (2006)
16. Sandeep, T., James, S.F., Anand, S.: Declarative Querying for Biological Sequences. In: Proceedings of the 22nd International Conference on Data Engineering (ICDE 2006). IEEE Computer Society, Los Alamitos (2006)
17. rCAD: Comparative RNA Analysis Database (manuscripts in preparation)
18. Yeang, C.H., et al.: Detecting the coevolution of biosequences-an example of RNA interaction prediction. Molecular biology and evolution 24(9), 2119-2131 (2007)
19. Gutell, R.R., Lee, J.C., Cannone, J.J.: The accuracy of ribosomal RNA comparative structure models. Curr. Opin. Struct. Biol. 12(3), 301-310 (2002)
20. Noller, H.F., et al.: Secondary structure model for 23S ribosomal RNA. Nucleic Acids Res. 9(22), 6167-6189 (1981)
21. Rzhetsky, A.: Estimating substitution rates in ribosomal RNA genes. Genetics 141(2), 771-783 (1995)
22. Hofacker, I.L., et al.: Automatic detection of conserved RNA structure elements in complete RNA virus genomes. Nucleic acids research 26(16), 3825-3836 (1998)
23. Knudsen, B., Hein, J.: RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. Bioinformatics 15(6), 446-454 (1999)
24. Rivas, E., et al.: Computational identification of noncoding RNAs in E. coli by comparative genomics. Current biology 11(17), 1369-1373 (2001)
25. di Bernardo, D., Down, T., Hubbard, T.: ddbrna: detection of conserved secondary structures in multiple alignments. Bioinformatics 19(13), 1606-1611 (2003)
26. Coventry, A., Kleitman, D.J., Berger, B.: MSARI: multiple sequence alignments for statistical detection of RNA secondary structure. Proceedings of the National Academy of Sciences of the United States of America 101(33), 12102-12107 (2004)
27. Washietl, S., et al.: Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. Nature biotechnology 23(11), 1383- 1390 (2005)
28. Pedersen, J.S., et al.: Identification and classification of conserved RNA secondary structures in the human genome. PLoS computational biology 2(4), e33 (2006)
29. Dutheil, J., et al.: A model-based approach for detecting coevolving positions in a molecule. Molecular biology and evolution 22(9), 1919-1928 (2005)
30. Felsenstein, J.: Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17(6), 368-376 (1981)
31. Ranwez, V., Gascuel, O.: Quartet-Based Phylogenetic Inference: Improvements and Limits. Molecular biology and evolution 18(6), 1103-1116 (2001)
32. Atchley, W.R., et al.: Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis. Molecular biology and evolution 17(1), 164-178 (2000)
33. Tillier, E.R., Lui, T.W.: Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments. Bioinformatics 19(6), 750-755 (2003)
34. Comparative RNA Website, http://www.rna.ccbb.utexas.edu/
35. PHYLIP, http://evolution.genetics.washington.edu/phylip.html
36. Gautheret, D., Damberger, S.H., Gutell, R.R.: Identification of base-triples in RNA using comparative sequence analysis. J. Mol. Biol. 248(1), 27-43 (1995)
37. Gutell, R.R.: Collection of small subunit (16S- and 16S-like) ribosomal RNA structures. Nucleic Acids Res. 21(13), 3051-3054 (1993)
38. Woese, C.R., et al.: Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids. Microbiol. Rev. 47(4), 621-669 (1983)
39. Patterson, D.A., Hennessy, J.L.: Computer architecture: a quantitative approach, vol. xxviii, 594, p. 160. Morgan Kaufman Publishers, San Mateo (1990)