Freiburg RNA Tools: A web server integrating IntaRNA, ExpaRNA and LocARNA

Nucleic Acids Research

Volumn 38, Issue SUPPL. 2, 2010, Pages

  Smith, Cameron ^a   Heyne, Steffen ^a   Richter, Andreas S ^a   Will, Sebastian ^a,b   Backofen, Rolf ^a  

^a UNIVERSITY OF FREIBURG   (Germany)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA; MESSENGER RNA; UNTRANSLATED RNA;

ARTICLE; BASE MISPAIRING; COMPUTER INTERFACE; COMPUTER PREDICTION; COMPUTER PROGRAM; GENE INTERACTION; PRIORITY JOURNAL; RNA ANALYSIS; RNA INTEGRATION; SEQUENCE ALIGNMENT; WEB BROWSER; CHEMISTRY; CONFORMATION; INTERNET; METABOLISM; SEQUENCE ANALYSIS; SYSTEM ANALYSIS;

INTERNET; NUCLEIC ACID CONFORMATION; RNA; RNA, MESSENGER; RNA, UNTRANSLATED; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA; SOFTWARE; SYSTEMS INTEGRATION;

EID: 77954269050     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq316     Document Type: Article

References (30)

1. Sharp,P.A. (2009) The centrality of RNA. Cell, 136, 577-580.
2. Amaral,P.P., Dinger,M.E., Mercer,T.R. and Mattick,J.S. (2008) The eukaryotic genome as an RNA machine. Science, 319, 1787-1789.
3. Washietl,S., Pedersen,J.S., Korbel,J.O., Stocsits,C., Gruber,A.R., Hackermüller,J., Hertel,J., Lindemeyer,M., Reiche,K., Tanzer,A. et al. (2007) Structured RNAs in the ENCODE selected regions of the human genome. Genome Res., 17, 852-864.
4. Serganov,A. and Patel,D.J. (2007) Ribozymes, riboswitches and beyond: regulation of gene expression without proteins. Nat. Rev. Genet., 8, 776-790.
5. Mattick,J.S. and Makunin,I.V. (2006) Non-coding RNA. Hum. Mol. Genet., 15, R17-R29.
6. Fröhlich,K.S. and Vogel,J. (2009) Activation of gene expression by small RNA. Curr. Opin. Microbiol., 12, 674-682.
7. 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.
8. Heyne,S., Will,S., Beckstette,M. and Backofen,R. (2009) Lightweight comparison of RNAs based on exact sequence-structure matches. Bioinformatics, 25, 2095-2102.
9. Will,S., Reiche,K., Hofacker,I.L., Stadler,P.F. and Backofen,R. (2007) Inferring non-coding RNA families and classes by means of genome-scale structure-based clustering. PLoS Comput. Biol., 3, e65.
10. Richter,A.S., Schleberger,C., Backofen,R. and Steglich,C. (2010) Seed-based IntaRNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1. Bioinformatics, 26, 1-5.
11. Gruber,A.R., Kilgus,C., Mosig,A., Hofacker,I.L., Hennig,W. and Stadler,P.F. (2008) Arthropod 7SK RNA. Mol. Biol. Evol., 25, 1923-1930.
12. Rose,D., Hackermüller,J., Washietl,S., Reiche,K., Hertel,J., Findeiss,S., Stadler,P.F. and Prohaska,S.J. (2007) Computational RNomics of drosophilids. BMC Genomics, 8, 406.
13. Gruber,A.R., Lorenz,R., Bernhart,S.H., Neubock,R. and Hofacker,I.L. (2008) The Vienna RNA websuite. Nucleic Acids Research, 36, W70-W74.
14. Zuker,M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
15. Mathews,D., Sabina,J., Zuker,M. and Turner,D. (1999) EXPAnded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol., 288, 911-940.
16. Hofacker,I.L., Fontana,W., Stadler,P.F., Bonhoeffer,S., Tacker,M. and Schuster,P. (1994) Fast folding and comparison of RNA secondary structures. Monatsh. Chem., 125, 167-188.
17. Mückstein,U., Tafer,H., Bernhart,S.H., Hernandez-Rosales,M., Vogel,J., Stadler,P.F. and Hofacker,I.L. (2008) Translational control by RNA-RNA interaction: improved computation of RNA-RNA binding thermodynamics. In Elloumi,M., Küng,J., Linial,M., Murphy,R., Schneider,K. and Toma,C. (eds), Bioinformatics Research and Development, of Communications in Computer and Information Science, Vol. 13. Springer-Verlag, Heidelberg, Berlin, Germany, pp. 114-127.
18. Bernhart,S.H., Hofacker,I.L. and Stadler,P.F. (2006) Local RNA base pairing probabilities in large sequences. Bioinformatics, 22, 614-615.
19. Brown,J.W. (1999) The ribonuclease P database. Nucleic Acids Res., 27, 314.
20. Heyne,S., Will,S., Beckstette,M. and Backofen,R. (2008) Proceedings of the German Conference on Bioinformatics (GCB'2008), Vol. P-136 of Lecture Notes in Informatics (LNI), Gesellschaft für Informatik (GI), Bonn, Germany, pp. 189-198.
21. Backofen,R. and Siebert,S. (2007) Fast detection of common sequence structure patterns in RNAs. J. Discrete Algorithms, 5, 212-228.
22. Höchsmann,M., Töller,T., Giegerich,R. and Kurtz,S. (2003) Proceedings of Computational Systems Bioinformatics (CSB 2003), Vol. 2, IEEE Computer Society, Los Alamitos, CA, USA, pp. 159-168.
23. Wilm,A., Mainz,I. and Steger,G. (2006) An enhanced RNA alignment benchmark for sequence alignment programs. Algorithms Mol. Biol., 1, 19.
24. Harmanci,A.O., Sharma,G. and Mathews,D.H. (2007) Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign. BMC Bioinformatics, 8, 130.
25. Torarinsson,E., Havgaard,J.H. and Gorodkin,J. (2007) Multiple structural alignment and clustering of RNA sequences. Bioinformatics, 23, 926-932.
26. Bauer,M., Klau,G.W. and Reinert,K. (2007) Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization. BMC Bioinformatics, 8, 271.
27. Sankoff,D. (1985) Simultaneous solution of the RNA folding, alignment and protosequence problems. SIAM J. Appl. Math., 45, 810-825.
28. Bernhart,S.H., Hofacker,I.L., Will,S., Gruber,A.R. and Stadler,P.F. (2008) RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics, 9, 474.
29. Otto,W., Will,S. and Backofen,R. (2008) Proceedings of German Conference on Bioinformatics (GCB'2008), Vol. P-136 of Lecture Notes in Informatics (LNI), Gesellschaft für Informatik (GI), Bonn, Germany, pp. 178-188.
30. Mann,M., Smith,C., Rabbath,M., Edwards,M., Will,S. and Backofen,R. (2009) CPSP-web-tools: a server for 3D lattice protein studies. Bioinformatics, 25, 676-677.