Beyond Mfold: recent advances in RNA bioinformatics

Reeder J, Höchsmann M, Rehmsmeier M, Voss B, Giegerich R (2006)
JOURNAL OF BIOTECHNOLOGY 124(1): 41-55.

Download
Es wurde kein Volltext hochgeladen. Nur Publikationsnachweis!
Konferenzbeitrag | Veröffentlicht | Englisch
Autor
; ; ; ;
Abstract / Bemerkung
Computational analysis of RNA secondary structure is a classical field of biosequence analysis, which has recently gained momentum due to the manyfold regulatory functions of RNA that have become apparent. We present five recent computational approaches that address the problems of synoptic folding space analysis, pseudoknot prediction, structure alignment, comparative structure prediction, and miRNA target prediction. All these programs are in current use and are available via the Bielefeld Bioinformatics Server at http://bibiserv.techfak.uni-bielefeld.de. (c) 2006 Elsevier B.V. All rights reserved.
Erscheinungsjahr
Band
124
Ausgabe
1
Seite(n)
41-55
ISSN
PUB-ID

Zitieren

Reeder J, Höchsmann M, Rehmsmeier M, Voss B, Giegerich R. Beyond Mfold: recent advances in RNA bioinformatics. JOURNAL OF BIOTECHNOLOGY. 2006;124(1):41-55.
Reeder, J., Höchsmann, M., Rehmsmeier, M., Voss, B., & Giegerich, R. (2006). Beyond Mfold: recent advances in RNA bioinformatics. JOURNAL OF BIOTECHNOLOGY, 124(1), 41-55. doi:10.1016/j.jbiotec.2006.01.034
Reeder, J., Höchsmann, M., Rehmsmeier, M., Voss, B., and Giegerich, R. (2006). Beyond Mfold: recent advances in RNA bioinformatics. JOURNAL OF BIOTECHNOLOGY 124, 41-55.
Reeder, J., et al., 2006. Beyond Mfold: recent advances in RNA bioinformatics. JOURNAL OF BIOTECHNOLOGY, 124(1), p 41-55.
J. Reeder, et al., “Beyond Mfold: recent advances in RNA bioinformatics”, JOURNAL OF BIOTECHNOLOGY, vol. 124, 2006, pp. 41-55.
Reeder, J., Höchsmann, M., Rehmsmeier, M., Voss, B., Giegerich, R.: Beyond Mfold: recent advances in RNA bioinformatics. JOURNAL OF BIOTECHNOLOGY. 124, 41-55 (2006).
Reeder, Jens, Höchsmann, Matthias, Rehmsmeier, Marc, Voss, Björn, and Giegerich, Robert. “Beyond Mfold: recent advances in RNA bioinformatics”. JOURNAL OF BIOTECHNOLOGY 124.1 (2006): 41-55.

37 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

GARN2: coarse-grained prediction of 3D structure of large RNA molecules by regret minimization.
Boudard M, Barth D, Bernauer J, Denise A, Cohen J., Bioinformatics 33(16), 2017
PMID: 28398456
Bridging the gap between in vitro and in vivo RNA folding.
Leamy KA, Assmann SM, Mathews DH, Bevilacqua PC., Q Rev Biophys 49(), 2016
PMID: 27658939
New insights from cluster analysis methods for RNA secondary structure prediction.
Rogers E, Heitsch C., Wiley Interdiscip Rev RNA 7(3), 2016
PMID: 26971529
Detecting riboSNitches with RNA folding algorithms: a genome-wide benchmark.
Corley M, Solem A, Qu K, Chang HY, Laederach A., Nucleic Acids Res 43(3), 2015
PMID: 25618847
GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies.
Boudard M, Bernauer J, Barth D, Cohen J, Denise A., PLoS One 10(8), 2015
PMID: 26313379
Using the RNAstructure Software Package to Predict Conserved RNA Structures.
Mathews DH., Curr Protoc Bioinformatics 46(), 2014
PMID: 24939126
Candidate gene association studies: a comprehensive guide to useful in silico tools.
Patnala R, Clements J, Batra J., BMC Genet 14(), 2013
PMID: 23656885
Deciphering the rules by which 5'-UTR sequences affect protein expression in yeast.
Dvir S, Velten L, Sharon E, Zeevi D, Carey LB, Weinberger A, Segal E., Proc Natl Acad Sci U S A 110(30), 2013
PMID: 23832786
Evaluating our ability to predict the structural disruption of RNA by SNPs.
Ritz J, Martin JS, Laederach A., BMC Genomics 13 Suppl 4(), 2012
PMID: 22759654
Inhibition of HIV-1 Integrase gene expression by 10-23 DNAzyme.
Singh N, Ranjan A, Sur S, Chandra R, Tandon V., J Biosci 37(3), 2012
PMID: 22750986
Folding RNA/DNA hybrid duplexes.
Lorenz R, Hofacker IL, Bernhart SH., Bioinformatics 28(19), 2012
PMID: 22829626
Predicting pseudoknotted structures across two RNA sequences.
Sperschneider J, Datta A, Wise MJ., Bioinformatics 28(23), 2012
PMID: 23044552
Heuristic RNA pseudoknot prediction including intramolecular kissing hairpins.
Sperschneider J, Datta A, Wise MJ., RNA 17(1), 2011
PMID: 21098139
Evaluation of the information content of RNA structure mapping data for secondary structure prediction.
Quarrier S, Martin JS, Davis-Neulander L, Beauregard A, Laederach A., RNA 16(6), 2010
PMID: 20413617
SHAPE-directed RNA secondary structure prediction.
Low JT, Weeks KM., Methods 52(2), 2010
PMID: 20554050
Disease-associated mutations that alter the RNA structural ensemble.
Halvorsen M, Martin JS, Broadaway S, Laederach A., PLoS Genet 6(8), 2010
PMID: 20808897
RNA structure prediction from evolutionary patterns of nucleotide composition.
Smit S, Knight R, Heringa J., Nucleic Acids Res 37(5), 2009
PMID: 19129237
Computational methods in noncoding RNA research.
Machado-Lima A, del Portillo HA, Durham AM., J Math Biol 56(1-2), 2008
PMID: 17786447
High-level expression of the native barley alpha-amylase/subtilisin inhibitor in Pichia pastoris.
Micheelsen PO, Ostergaard PR, Lange L, Skjøt M., J Biotechnol 133(4), 2008
PMID: 18207271
RnaPredict--an evolutionary algorithm for RNA secondary structure prediction.
Wiese KC, Deschenes AA, Hendriks AG., IEEE/ACM Trans Comput Biol Bioinform 5(1), 2008
PMID: 18245873
R-Coffee: a method for multiple alignment of non-coding RNA.
Wilm A, Higgins DG, Notredame C., Nucleic Acids Res 36(9), 2008
PMID: 18420654
ConStruct: Improved construction of RNA consensus structures.
Wilm A, Linnenbrink K, Steger G., BMC Bioinformatics 9(), 2008
PMID: 18442401
Common evolutionary trends for SINE RNA structures.
Sun FJ, Fleurdépine S, Bousquet-Antonelli C, Caetano-Anollés G, Deragon JM., Trends Genet 23(1), 2007
PMID: 17126948
RNA localization signals: deciphering the message with bioinformatics.
Hamilton RS, Davis I., Semin Cell Dev Biol 18(2), 2007
PMID: 17452113
RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints.
Chung YS, Lee WH, Tang CY, Lu CL., Nucleic Acids Res 35(web server issue), 2007
PMID: 17488842
Informatics challenges in structured RNA.
Laederach A., Brief Bioinform 8(5), 2007
PMID: 17611237
MicroRNA-mediated regulation of stomatal development in Arabidopsis.
Kutter C, Schöb H, Stadler M, Meins F, Si-Ammour A., Plant Cell 19(8), 2007
PMID: 17704216
RNAspa: a shortest path approach for comparative prediction of the secondary structure of ncRNA molecules.
Horesh Y, Doniger T, Michaeli S, Unger R., BMC Bioinformatics 8(), 2007
PMID: 17908318

33 References

Daten bereitgestellt von Europe PubMed Central.

Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots
Akutsu, Discrete Appl. Math. 104(), 2000
Secondary structure prediction of interacting RNA molecules.
Andronescu M, Zhang ZC, Condon A., J. Mol. Biol. 345(5), 2004
PMID: 15644199
A statistical sampling algorithm for RNA secondary structure prediction.
Ding Y, Lawrence CE., Nucleic Acids Res. 31(24), 2003
PMID: 14654704
Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction
Doshi, BMC Bioinformatics 5(105), 2004
A comprehensive comparison of comparative RNA structure prediction approaches
Gardner, BMC Bioinformatics 5(140), 2004
A discipline of dynamic programming over sequence data
Giegerich, Sci. Comput. Program. 51(3), 2004
Abstract shapes of RNA.
Giegerich R, Voss B, Rehmsmeier M., Nucleic Acids Res. 32(16), 2004
PMID: 15371549
Finding the most significant common sequence and structure motifs in a set of RNA sequences.
Gorodkin J, Heyer LJ, Stormo GD., Nucleic Acids Res. 25(18), 1997
PMID: 9278497
Rfam: an RNA family database.
Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR., Nucleic Acids Res. 31(1), 2003
PMID: 12520045
Local similarity in RNA secondary structures
Höchsmann, 2003
Pure multiple RNA secondary structure alignments: a progressive profile approach.
Hochsmann M, Voss B, Giegerich R., IEEE/ACM Trans Comput Biol Bioinform 1(1), 2004
PMID: 17048408
Vienna RNA secondary structure server.
Hofacker IL., Nucleic Acids Res. 31(13), 2003
PMID: 12824340
Fast folding and comparison of RNA secondary structures
Hofacker, Monatsh. Chem. 125(), 1994
A heuristic approach for detecting RNA H-type pseudoknots.
Huang CH, Lu CL, Chiu HT., Bioinformatics 21(17), 2005
PMID: 15994188
Alignment of trees an alternative to tree edit
Jiang, Theor. Comput. Sci. 143(1), 1995
RNA pseudoknot prediction in energy-based models.
Lyngso RB, Pedersen CN., J. Comput. Biol. 7(3-4), 2000
PMID: 11108471
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.
Mathews DH, Sabina J, Zuker M, Turner DH., J. Mol. Biol. 288(5), 1999
PMID: 10329189
A three-stemmed mRNA pseudoknot in the SARS coronavirus frameshift signal.
Plant EP, Perez-Alvarado GC, Jacobs JL, Mukhopadhyay B, Hennig M, Dinman JD., PLoS Biol. 3(6), 2005
PMID: 15884978
Fast and effective prediction of microRNA/target duplexes.
Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R., RNA 10(10), 2004
PMID: 15383676
Simultaneous solution of the RNA folding, alignment and protosequence problems
Sankoff, SIAM J. Appl. Math. 45(5), 1985
A massively parallel genetic algorithm for RNA secondary structure prediction
Shapiro, J. Supercomput. 8(), 1994
Identification of Drosophila MicroRNA targets.
Stark A, Brennecke J, Russell RB, Cohen SM., PLoS Biol. 1(3), 2003
PMID: 14691535
An RNA folding method capable of identifying pseudoknots and base triples.
Tabaska JE, Cary RB, Gabow HN, Stormo GD., Bioinformatics 14(8), 1998
PMID: 9789095
On the complexity of multiple sequence alignment.
Wang L, Jiang T., J. Comput. Biol. 1(4), 1994
PMID: 8790475
Complete suboptimal folding of RNA and the stability of secondary structures.
Wuchty S, Fontana W, Hofacker IL, Schuster P., Biopolymers 49(2), 1999
PMID: 10070264

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 16530285
PubMed | Europe PMC

Suchen in

Google Scholar