RNApredator: Fast accessibility-based prediction of sRNA targets

Nucleic Acids Research

Volumn 39, Issue SUPPL. 2, 2011, Pages

  Eggenhofer, Florian ^a   Tafer, Hakim ^b   Stadler, Peter F ^a,b,c,d,e,f   Hofacker, Ivo L ^a,e  

^a UNIVERSITY OF VIENNA   (Austria)

^b UNIVERSITY OF LEIPZIG   (Germany)

^c MAX PLANCK INSTITUTE FOR MATHEMATICS IN THE SCIENCES   (Germany)

^d FRAUNHOFER INSTITUTE FOR CELL THERAPY AND IMMUNOLOGY   (Germany)

^e UNIVERSITY OF COPENHAGEN   (Denmark)

^f SANTA FE INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; TRANSFER RNA;

ALGORITHM; ARTICLE; BACTERIAL GENOME; CLIENT SERVER APPLICATION; COMPUTER PROGRAM; INTERNAL RIBOSOME ENTRY SITE; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; PREDICTION; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; RNA BINDING; RNA PROCESSING; RNA SEQUENCE; SENSITIVITY AND SPECIFICITY;

GENE EXPRESSION REGULATION, BACTERIAL; GENOME, BACTERIAL; RNA, BACTERIAL; RNA, MESSENGER; RNA, SMALL UNTRANSLATED; SEQUENCE ANALYSIS, RNA; SOFTWARE;

BACTERIA (MICROORGANISMS);

EID: 79959937873     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr467     Document Type: Article

References (28)

1. Vogel, J. and Sharma, C.M. (2005) How to find small non-coding RNAs in bacteria. Biol. Chem., 386, 1219-1238. (Pubitemid 41790806)
2. Livny, J., Brencic, A., Lory, S. and Waldor, M.K. (2006) Identification of 17 pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool sRNApredict2. Nucleic Acids Res., 34, 3484-3493.
3. Lease, R.A. and Belfort, M. (2000) A trans-acting RNA as a control switch in escherichia coli: Dsra modulates function by forming alternative structures. Proc. Natl Acad. Sci. USA, 97, 9919-9924.
4. Lease, R.A., Cusick, M.E. and Belfort, M. (1998) Riboregulation in escherichia coli: Dsra RNA acts by RNA:RNA interactions at multiple loci. Proc. Natl Acad. Sci. USA, 95, 12456-12461. (Pubitemid 28483786)
5. Majdalani, N., Chen, S., Murrow, J., St. John, K. and Gottesman, S. (2001) Regulation of RpoS by a novel small RNA: the characterization of RprA. Mol. Microbiol., 39, 1382-1394. (Pubitemid 32225146)
6. Chen, S., Zhang, A., Blyn, L.B. and Storz, G. (2004) MicC, a second small RNA regulator of Omp protein expression in escherichia coli. J. Bacteriol., 186, 6689-6697. (Pubitemid 39332105)
7. Vogel, J., Argaman, L., Wagner, E.G. and Altuvia, S. (2004) The small RNA istr inhibits synthesis of an sos-induced toxic peptide. Curr. Biol., 14, 2271-2276. (Pubitemid 40033365)
8. Tjaden, B., Goodwin, S.S., Opdyke, J.A., Guillier, M., Fu, D.X., Gottesman, S. and Storz, G. (2006) Target prediction for small, noncoding RNAs in bacteria. Nucleic Acids Res., 34, 2791-2802. (Pubitemid 43985640)
9. Tjaden, B. (2008) TargetRNA: a tool for predicting targets of small RNA action in bacteria. Nucleic Acids Res., 36, 109-113.
10. Smith, T.F. and Waterman, M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
11. Mandin, P., Repoila, F., Vergassola, M., Geissmann, T. and Cossart, P. (2007) Identification of new noncoding RNAs in listeria monocytogenes and prediction of mRNA targets. Nucleic Acids Res., 35, 962-974. (Pubitemid 46344721)
12. Zuker, M. and Stiegler, P. (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res., 9, 133-148.
13. Mathews, D.H., Burkard, M.E., Freier, S.M., Wyatt, J.R. and Turner, D.H. (1999) Predicting oligonucleotide affinity to nucleic acid targets. RNA, 5, 1458-1469. (Pubitemid 29530490)
14. Busch, A., Richter, A.S. and Backofen, R. (2008) IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics, 24, 2849-2856.
15. Mü ckstein, U., Tafer, H., Hackermü ller, J., Bernhart, S.H., Stadler, P.F. and Hofacker, I.L. (2006) Thermodynamics of RNA-RNA binding. Bioinformatics, 22, 1177-1182. (Pubitemid 43779008)
16. Mü ckstein, U., Tafer, H., Bernhart, S.H., Hernandez-Rosales, M., Vogel, J., Stadler, P.F. and Hofacker, I.L.Translational control by RNA-RNA interaction: Improved computation of RNA-RNA binding thermodynamics. In Elloumi, M., Kö ng, J., Linial, M., Murphy, R.F., Schneider, K. and Toma, C. (eds), Bioinformatics Research and Development, Vol. 13 of Communications in Computer and Information Science, pp. 114-127. Springer, Berlin Heidelberg, 2008.
17. Chitsaz, H., Salari, R., Sahinalp, S.C. and Backofen, R. (2009) A partition function algorithm for interacting nucleic acid strands. Bioinformatics, 25, 365-373.
18. Tafer, H. and Hofacker, I.L. (2008) RNAplex: a fast tool for RNA-RNA interaction search. Bioinformatics, 24, 2657-2663.
19. Thomas, M., Lieberman, J. and Lal, A. (2010) Desperately seeking microRNA targets. Nat. Struct. Mol. Biol., 17, 1169-1174.
20. Smith, C., Heyne, S., Richter, A.S., Will, S. and Backofen, R. (2010) Freiburg RNA tools: a web server integrating intaRNA, expaRNA and locaRNA. Nucleic Acids Res., 38, 373-377.
21. Gruber, A.R., Lorenz, R., Bernhart, S.H., Neubö ck, R. and Hofacker, I.L. (2008) The vienna RNA websuite. Nucleic Acids Res., 36, 70-74.
22. Papenfort, K., Said, N., Welsink, T., Lucchini, S., Hinton, J.C. and Vogel, J. (2009) Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA. Mol. Microbiol., 74, 139-158.
23. Pfeiffer, V., Papenfort, K., Lucchini, S., Hinton, J.C. and Vogel, J. (2009) Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation. Nat. Struct. Mol. Biol., 16, 840-846.
24. Sledjeski, D.D. and Gottesman, S. (1996) Osmotic shock induction of capsule synthesis in escherichia coli K-12. J. Bacteriol., 178, 1204-1206. (Pubitemid 26048042)
25. Alexa, A., Rahnenfü hrer, J. and Lengauer, T. (2006) Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics, 22, 1600-1607. (Pubitemid 43985293)
26. Bompfü nwerer, A.F., Backofen, R., Berhart, S.H., Hertel, J., Hofacker, I.L., Stadler, P.F. and Will, S. (2008) Variations on RNA folding and alignment: Lessons from Benasque. J. Math. Biol., 56, 129-144. (Pubitemid 350172187)
27. Berhart, S.H., Mü ckstein, U. and Hofacker, I.L. (2011) RNA Accessibility in cubic time. Algorithms. Mol Biol., 6, 3.
28. Tafer, H., Amman, F., Eggenhofer, F., Stadler, P.F. and Hofacker, I.L. (2011) Fast Accessiblity-Based Prediction of RNARNA Interactions. Bioinformatics (18 May, date last accessed).