Enhancement of accuracy and efficiency for RNA secondary structure prediction by sequence segmentation and MapReduce

BMC Structural Biology

Volumn 13, Issue SUPPL.1, 2013, Pages

  Zhang, Boyu ^a   Yehdego, Daniel T ^b   Johnson, Kyle L ^b   Leung, Ming Ying ^b   Taufer, Michela ^a  

^a University of Delaware   (United States)

^b UNIVERSITY OF TEXAS AT EL PASO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC RNA; VIRUS RNA;

ANALYTIC METHOD; ARTICLE; CENTERED CHUNKING METHOD; MAPREDUCE FRAMEWORK; NODAVIRUS; OPTIMIZED CHUNKING METHOD; PROTEIN SECONDARY STRUCTURE; REGULAR CHUNKING METHOD; RNA SEQUENCE; RNA STRUCTURE; SEQUENCE ANALYSIS; SEQUENCE SEGMENTATION; TURNAROUND TIME;

ALGORITHMS; BASE PAIRING; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; MODELS, MOLECULAR; NODAVIRIDAE; NUCLEIC ACID CONFORMATION; REPRODUCIBILITY OF RESULTS; RNA; RNA, VIRAL; SEQUENCE INVERSION;

EID: 84887470639     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-13-S1-S3     Document Type: Article

References (32)

1. The small RNA world. Finnegan E, Matzke M, Journal of Cell Science 2003 116 23 4689 4693 10.1242/jcs.00838 14600255
2. Mechanisms and enzymes involved in SARS coronavirus genome expression. Thiel V, Ivanov KA, Putics A, Hertziq T, Schelle B, Bayer S, Weissbrich B, Snijder EJ, Rabenau H, Doerr HW, Gorbalenya AE, Ziebuhr J, Journal of General Virology 2003 84 Pt 9 2305 2315 12917450
3. HotKnots: Heuristic prediction of RNA secondary structures including pseudoknots. Ren J, Rastegari B, Condon A, Hoos HH, RNA 2005 11 10 1494 1504 10.1261/rna.7284905 16199760
4. Viral RNA pseudoknots: Versatile motifs in gene expression and replication. Brierley I, Pennell S, Gilbert RJ, Nature Reviews Microbiology 2007 5 8 598 610 10.1038/nrmicro1704 17632571
5. Fast algorithm for predicting the secondary structure of single stranded RNA. Nussinov R, Jacobson A, Proceedings of the National Academy of Sciences of the United States of America 1980 77 11 6309 6313 10.1073/pnas.77.11.6309 6161375
6. Simultaneous solution of the RNA folding, alignment, and protosequence problems. Sankoff D, SIAM Journal on Applied Mathematics 1985 45 5 810 825 10.1137/0145048
7. Mfold web server for nucleic acid folding and hybridization prediction. Zuker M, Nucleic Acids Research 2003 31 13 3406 3415 10.1093/nar/gkg595 12824337
8. A dynamic programming algorithm for RNA structure prediction including pseudoknots. Rivas E, Eddy SR, Journal of Molecular Biology 1999 285 5 2053 2568 10.1006/jmbi.1998.2436 9925784
9. An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots. Dirks R, Pierce N, Journal of Computational Chemistry 2004 25 10 1295 1304 10.1002/jcc.20057 15139042
10. RNAVLab: a virtual laboratory for studying RNA secondary structures based on Grid computing technology. Taufer M, Leung MY, Solorio T, Licon A, Mireles D, Araiza R, Johnson K, Parallel Computing 2008 34 11 661 680 10.1016/j.parco.2008.08.002 19885376
11. A 3' terminal stem-loop structure in Nodamura virus RNA2 forms an essential cis-acting signal for RNA replication. Rosskopf JJ, III JHU, Rodarte L, Romero TA, Leung MY, Taufer M, Johnson KL, Virus Research 2010 150 1-2 12 21 10.1016/j.virusres.2010.02.006 20176063
12. Poster: Secondary structure predictions for long RNA sequences based on inversion excursions. Yehdego D, Kodimala V, Viswakula S, Zhang B, Vegesna R, Johnson K, Taufer M, Leung MY, Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine (BCB) 2012
13. Secondary structure predictions for long RNA sequences based on inversion excursions and MapReduce. Yehdego D, Zhang B, Kodimala VKR, Johnson K, Taufer M, Leung MY, Proceedings of 12th IEEE International Workshop on High Performance Computational Biology (HiCOMB) 2013
14. MapReduce: Simplified data processing on large clusters. Dean J, Ghemawat S, Proceedings of the 6th conference on Symposium on Opearting Systems Design and Implementation 2004
15. FX: an RNA-Seq analysis tool on the Cloud. Hong D, Rhie A, Park SS, Lee J, Ju YS, Kim S, Yu SB, Bleazard T, Park HS, Rhee H, Chong H, Yang KS, Lee YS, Kim IH, Lee JS, Kim JI, Seo JS, Bioinformatics 2012 28 5 721 723 10.1093/bioinformatics/bts023 22257667
16. Cloud-scale RNA-sequencing differential expression analysis with Myrna. Langmead B, Hansen KD, Leek JT, Genome Biol 2010 11 83 10.1186/gb-2010-11-8-r83 20701754
17. A modularized MapReduce framework to support RNA secondary structure prediction and analysis workflows. Zhang B, Yehdego D, Johnson K, Leung MY, Taufer M, Bioinformatics and Biomedicine Workshops (BIBMW), 2012 IEEE International Conference on: 4-7 October 2012 2012 86 93 10.1109/BIBMW.2012. 6470251
18. Emboss-palindrome. http://emboss.bioinformatics.nl/cgi-bin/emboss/ palindrome
19. Statistical composition of high-scoring segments from molecular sequences. Karlin S, Dembo A, Kawabata T, Annals of Statistics 1990 18 2 571 581 10.1214/aos/1176347616
20. AT excursion: a new approach to predict replication origins in viral genomes by locating AT-rich regions. Chew DS, Leung MY, Choi1 KP, BMC Bioinformatics 2007 8 163 10.1186/1471-2105-8-163 17517140
21. RFAM database. http://rfam.sanger.ac.uk/
22. MATLAB, Version 7.10.0.499 (R2010a) Natick, Massachusetts: The MathWorks Inc. 2010
23. The use of ranks to avoid the assumption of normality implicit in the analysis of variance. Friedman M, Journal of the American Statistical Association 1937 32 200 675 701 10.1080/01621459.1937.10503522
24. IPknot: Fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. Sato K, Kato Y, Hamada M, Akutsu T, Asai K, Bioinformatics 2011 27 13 85 i93 10.1093/bioinformatics/btr215 21685106
25. pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows. Reeder J, Steffen P, Giegerich R, Nucleic Acids Res 2007 35 320 W324 10.1093/nar/gkm258 17478505
26. A partition function algorithm for nucleic acid secondary structure including pseudoknots. Dirks R, Pierce NA, Journal of Computational Chemistry 2003 24 13 1664 1677 10.1002/jcc.10296 12926009
27. UNAFold: Software for nucleic acid folding and hybridization. Markham NR, Zuker M, Methods in Molecular Biology 2008 453 3 31 10.1007/978-1-60327-429-6-1 18712296
28. Fast folding and comparison of RNA secondary structures. Hofacker I, Fontana W, Stadler P, Bonhoeffer S, Tacker M, Schuster P, Monatshefte für Chemie 1994 125 167 188 10.1007/BF00818163
29. PseudoBase++: an extension of PseudoBase for easy searching, formatting, and visualization of pseudoknots. Taufer M, Licon A, Araiza R, Mireles D, van Batenburg FH, Gultyaev AP, Leung MY, Nucleic Acids Res 2009 37 Database issue 127 D135 10.1093/nar/gkn806 18988624
30. The sample correlation coefficient r. Snedecor GW, Cochran WG, Statistical Methods Ames, IA: Iowa State Press 7 1980 175 178
31. Comparisons among the larger genome segments of six Nodaviruses and their encoded RNA replicases. Johnson KN, Johnson KL, Dasgupta R, Gratsch T, Ball LA, Journal of General Virology 2001 82 Pt 8 1855 1866 11457991
32. Family Nodaviridae. Thiery R, Johnson KL, Nakai T, Schneemann A, Bonami JR, Lightner DV, Virus Taxonomy Ninth Report of the International Committee on Taxonomy of Viruses Elsevier Academic Press, King AM, Lefkowitz E, Adams MJ, Carstens EB, Waltham, MA, 2011 1061 1067