Beyond Mfold: recent advances in RNA bioinformatics
Reeder J, Höchsmann M, Rehmsmeier M, Voss B, Giegerich R (2006)
In: Journal of Biotechnology. JOURNAL OF BIOTECHNOLOGY, 124(1). ELSEVIER SCIENCE BV: 41-55.
Konferenzbeitrag
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Autor*in
Reeder, Jens;
Höchsmann, Matthias;
Rehmsmeier, MarcUniBi;
Voss, Björn;
Giegerich, RobertUniBi
Einrichtung
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.
Stichworte
consensus structure prediction;
RNA interference;
structure comparison;
RNA;
miRNA target prediction;
RNA pseudoknots;
RNA secondary structure
Erscheinungsjahr
2006
Titel des Konferenzbandes
Journal of Biotechnology
Serien- oder Zeitschriftentitel
JOURNAL OF BIOTECHNOLOGY
Band
124
Ausgabe
1
Seite(n)
41-55
ISSN
0168-1656
Page URI
https://pub.uni-bielefeld.de/record/1598807
Zitieren
Reeder J, Höchsmann M, Rehmsmeier M, Voss B, Giegerich R. Beyond Mfold: recent advances in RNA bioinformatics. In: Journal of Biotechnology. JOURNAL OF BIOTECHNOLOGY. Vol 124. ELSEVIER SCIENCE BV; 2006: 41-55.
Reeder, J., Höchsmann, M., Rehmsmeier, M., Voss, B., & Giegerich, R. (2006). Beyond Mfold: recent advances in RNA bioinformatics. Journal of Biotechnology, JOURNAL OF BIOTECHNOLOGY, 124, 41-55. ELSEVIER SCIENCE BV. https://doi.org/10.1016/j.jbiotec.2006.01.034
Reeder, Jens, Höchsmann, Matthias, Rehmsmeier, Marc, Voss, Björn, and Giegerich, Robert. 2006. “Beyond Mfold: recent advances in RNA bioinformatics”. In Journal of Biotechnology, 124:41-55. JOURNAL OF BIOTECHNOLOGY. ELSEVIER SCIENCE BV.
Reeder, J., Höchsmann, M., Rehmsmeier, M., Voss, B., and Giegerich, R. (2006). “Beyond Mfold: recent advances in RNA bioinformatics” in Journal of Biotechnology JOURNAL OF BIOTECHNOLOGY, vol. 124, (ELSEVIER SCIENCE BV), 41-55.
Reeder, J., et al., 2006. Beyond Mfold: recent advances in RNA bioinformatics. In Journal of Biotechnology. JOURNAL OF BIOTECHNOLOGY. no.124 ELSEVIER SCIENCE BV, pp. 41-55.
J. Reeder, et al., “Beyond Mfold: recent advances in RNA bioinformatics”, Journal of Biotechnology, JOURNAL OF BIOTECHNOLOGY, vol. 124, ELSEVIER SCIENCE BV, 2006, pp.41-55.
Reeder, J., Höchsmann, M., Rehmsmeier, M., Voss, B., Giegerich, R.: Beyond Mfold: recent advances in RNA bioinformatics. Journal of Biotechnology. JOURNAL OF BIOTECHNOLOGY. 124, p. 41-55. ELSEVIER SCIENCE BV (2006).
Reeder, Jens, Höchsmann, Matthias, Rehmsmeier, Marc, Voss, Björn, and Giegerich, Robert. “Beyond Mfold: recent advances in RNA bioinformatics”. Journal of Biotechnology. ELSEVIER SCIENCE BV, 2006.Vol. 124. JOURNAL OF BIOTECHNOLOGY. 41-55.
37 Zitationen in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
Conditioning and Robustness of RNA Boltzmann Sampling under Thermodynamic Parameter Perturbations.
Rogers E, Murrugarra D, Heitsch C., Biophys J 113(2), 2017
PMID: 28629618
Rogers E, Murrugarra D, Heitsch C., Biophys J 113(2), 2017
PMID: 28629618
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
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
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
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
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
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
Mathews DH., Curr Protoc Bioinformatics 46(), 2014
PMID: 24939126
Structural characterization of the internal transcribed spacer 2 (ITS2) of the ribosomal DNA (rDNA) cluster in Calyptratae (Diptera: Schizophora) and its implications for molecular phylogenetic analyses.
Marinho MA, Azeredo-Espin AM, Zanchin NI., J Mol Evol 76(3), 2013
PMID: 23420176
Marinho MA, Azeredo-Espin AM, Zanchin NI., J Mol Evol 76(3), 2013
PMID: 23420176
Candidate gene association studies: a comprehensive guide to useful in silico tools.
Patnala R, Clements J, Batra J., BMC Genet 14(), 2013
PMID: 23656885
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
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
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
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
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
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
Sperschneider J, Datta A, Wise MJ., RNA 17(1), 2011
PMID: 21098139
Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation.
Bernauer J, Huang X, Sim AY, Levitt M., RNA 17(6), 2011
PMID: 21521828
Bernauer J, Huang X, Sim AY, Levitt M., RNA 17(6), 2011
PMID: 21521828
Electrochemical genosensors for the detection of Bonamia parasite. Selection of single strand-DNA (ssDNA) probes by simulation of the secondary structure folding.
Narcisi V, Mascini M, Perez G, Del Carlo M, Tiscar PG, Yamanaka H, Compagnone D., Talanta 85(4), 2011
PMID: 21872040
Narcisi V, Mascini M, Perez G, Del Carlo M, Tiscar PG, Yamanaka H, Compagnone D., Talanta 85(4), 2011
PMID: 21872040
Annexin A2 binds RNA and reduces the frameshifting efficiency of infectious bronchitis virus.
Kwak H, Park MW, Jeong S., PLoS One 6(8), 2011
PMID: 21918681
Kwak H, Park MW, Jeong S., PLoS One 6(8), 2011
PMID: 21918681
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
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
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
Halvorsen M, Martin JS, Broadaway S, Laederach A., PLoS Genet 6(8), 2010
PMID: 20808897
SARNA-Predict: accuracy improvement of RNA secondary structure prediction using permutation-based simulated annealing.
Tsang HH, Wiese KC., IEEE/ACM Trans Comput Biol Bioinform 7(4), 2010
PMID: 21030739
Tsang HH, Wiese KC., IEEE/ACM Trans Comput Biol Bioinform 7(4), 2010
PMID: 21030739
RNA structure prediction from evolutionary patterns of nucleotide composition.
Smit S, Knight R, Heringa J., Nucleic Acids Res 37(5), 2009
PMID: 19129237
Smit S, Knight R, Heringa J., Nucleic Acids Res 37(5), 2009
PMID: 19129237
Predicting structures and stabilities for H-type pseudoknots with interhelix loops.
Cao S, Chen SJ., RNA 15(4), 2009
PMID: 19237463
Cao S, Chen SJ., RNA 15(4), 2009
PMID: 19237463
Computational methods in noncoding RNA research.
Machado-Lima A, del Portillo HA, Durham AM., J Math Biol 56(1-2), 2008
PMID: 17786447
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
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
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
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
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
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
Hamilton RS, Davis I., Semin Cell Dev Biol 18(2), 2007
PMID: 17452113
Analysis of tRNA abstract shapes of precursor/derivative amino acids in Archaea.
Burbano HA, Andrade E., Gene 396(1), 2007
PMID: 17433860
Burbano HA, Andrade E., Gene 396(1), 2007
PMID: 17433860
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
Chung YS, Lee WH, Tang CY, Lu CL., Nucleic Acids Res 35(web server issue), 2007
PMID: 17488842
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
Kutter C, Schöb H, Stadler M, Meins F, Si-Ammour A., Plant Cell 19(8), 2007
PMID: 17704216
Prediction of RNA pseudoknots using heuristic modeling with mapping and sequential folding.
Dawson WK, Fujiwara K, Kawai G., PLoS One 2(9), 2007
PMID: 17878940
Dawson WK, Fujiwara K, Kawai G., PLoS One 2(9), 2007
PMID: 17878940
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
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
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
Andronescu M, Zhang ZC, Condon A., J. Mol. Biol. 345(5), 2004
PMID: 15644199
RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble.
Ding Y, Chan CY, Lawrence CE., RNA 11(8), 2005
PMID: 16043502
Ding Y, Chan CY, Lawrence CE., RNA 11(8), 2005
PMID: 16043502
A statistical sampling algorithm for RNA secondary structure prediction.
Ding Y, Lawrence CE., Nucleic Acids Res. 31(24), 2003
PMID: 14654704
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
Doshi, BMC Bioinformatics 5(105), 2004
A comprehensive comparison of comparative RNA structure prediction approaches
Gardner, BMC Bioinformatics 5(140), 2004
Gardner, BMC Bioinformatics 5(140), 2004
A discipline of dynamic programming over sequence data
Giegerich, Sci. Comput. Program. 51(3), 2004
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
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
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
Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR., Nucleic Acids Res. 31(1), 2003
PMID: 12520045
Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods.
Gutell RR, Power A, Hertz GZ, Putz EJ, Stormo GD., Nucleic Acids Res. 20(21), 1992
PMID: 1454539
Gutell RR, Power A, Hertz GZ, Putz EJ, Stormo GD., Nucleic Acids Res. 20(21), 1992
PMID: 1454539
Local similarity in RNA secondary structures
Höchsmann, 2003
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
Hochsmann M, Voss B, Giegerich R., IEEE/ACM Trans Comput Biol Bioinform 1(1), 2004
PMID: 17048408
Fast folding and comparison of RNA secondary structures
Hofacker, Monatsh. Chem. 125(), 1994
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
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
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
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
Mathews DH, Sabina J, Zuker M, Turner DH., J. Mol. Biol. 288(5), 1999
PMID: 10329189
Dynalign: an algorithm for finding the secondary structure common to two RNA sequences.
Mathews DH, Turner DH., J. Mol. Biol. 317(2), 2002
PMID: 11902836
Mathews DH, Turner DH., J. Mol. Biol. 317(2), 2002
PMID: 11902836
The equilibrium partition function and base pair binding probabilities for RNA secondary structure.
McCaskill JS., Biopolymers 29(6-7), 1990
PMID: 1695107
McCaskill JS., Biopolymers 29(6-7), 1990
PMID: 1695107
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
Plant EP, Perez-Alvarado GC, Jacobs JL, Mukhopadhyay B, Hennig M, Dinman JD., PLoS Biol. 3(6), 2005
PMID: 15884978
Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics.
Reeder J, Giegerich R., BMC Bioinformatics 5(), 2004
PMID: 15294028
Reeder J, Giegerich R., BMC Bioinformatics 5(), 2004
PMID: 15294028
Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction.
Reeder J, Giegerich R., Bioinformatics 21(17), 2005
PMID: 16020472
Reeder J, Giegerich R., Bioinformatics 21(17), 2005
PMID: 16020472
Fast and effective prediction of microRNA/target duplexes.
Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R., RNA 10(10), 2004
PMID: 15383676
Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R., RNA 10(10), 2004
PMID: 15383676
A dynamic programming algorithm for RNA structure prediction including pseudoknots.
Rivas E, Eddy SR., J. Mol. Biol. 285(5), 1999
PMID: 9925784
Rivas E, Eddy SR., J. Mol. Biol. 285(5), 1999
PMID: 9925784
Simultaneous solution of the RNA folding, alignment and protosequence problems
Sankoff, SIAM J. Appl. Math. 45(5), 1985
Sankoff, SIAM J. Appl. Math. 45(5), 1985
A massively parallel genetic algorithm for RNA secondary structure prediction
Shapiro, J. Supercomput. 8(), 1994
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
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
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
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
Wuchty S, Fontana W, Hofacker IL, Schuster P., Biopolymers 49(2), 1999
PMID: 10070264
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information.
Zuker M, Stiegler P., Nucleic Acids Res. 9(1), 1981
PMID: 6163133
Zuker M, Stiegler P., Nucleic Acids Res. 9(1), 1981
PMID: 6163133
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