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Comparative methods for RNA structure analysis - Part 1
Multi angle
Authors : Will, Sebastian (Author of the conference)
CIRM (Publisher )
68Q25 - Analysis of algorithms and problem complexity
68T05 - Learning and adaptive systems
92C40 - Biochemistry, molecular biology
92D10 - Genetics
92D20 - Protein sequences, DNA sequences
92E10 - Molecular structure (graph-theoretic methods, methods of differential topology, etc.)
Additional resources :
https://www.cirm-math.fr/ProgWeebly/2019/Renc1999/Will.pdf
https://www.tbi.univie.ac.at/~will/AlgoSB19/
CIRM (Publisher )
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Abstract :
Keywords : RNA structure; RNA alignment; sequence alignment; secondary structure; pairwise alignment; input alignment; ncRNA gene; multiple alignment; consensus structure; folding energy; computational models; simultaneous alignment and folding
MSC Codes : 68Q25 - Analysis of algorithms and problem complexity
68T05 - Learning and adaptive systems
92C40 - Biochemistry, molecular biology
92D10 - Genetics
92D20 - Protein sequences, DNA sequences
92E10 - Molecular structure (graph-theoretic methods, methods of differential topology, etc.)
Additional resources :
https://www.cirm-math.fr/ProgWeebly/2019/Renc1999/Will.pdf
https://www.tbi.univie.ac.at/~will/AlgoSB19/
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Information on the Video
Film maker : Hennenfent, GuillaumeLanguage : English Available date : 23/01/2019 Conference Date : 17/01/2019 Subseries : Research School arXiv category : Quantitative Biology ; Computer Science Mathematical Area(s) : Mathematics in Science & Technology ; Computer Science Format : MP4 (.mp4) - HD Video Time : 01:02:08 Targeted Audience : Researchers ; Graduate Students Download : https://videos.cirm-math.fr/2019-01-17_Will_1.mp4 
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Information on the Event
Event Title : AlgoSB 2019 - Mathematical and computational methods for structured RiboNucleic Acids / AlgoSB 2019 - Méthodes mathématiques et informatiques pour les Acides RiboNucléiques structurésEvent Organizers : Ponty, Yann ; Tanzer, Andrea Dates : 14/01/2019 - 18/01/2019 Event Year : 2019 Event URL : https://conferences.cirm-math.fr/1999.html
Citation Data
DOI : 10.24350/CIRM.V.19487803Cite this video as: Will, Sebastian (2019). Comparative methods for RNA structure analysis - Part 1. CIRM. Audiovisual resource. doi:10.24350/CIRM.V.19487803 URI : http://dx.doi.org/10.24350/CIRM.V.19487803 |
See Also
- [Multi angle] Comparative methods for RNA structure analysis - Part 2 / Author of the conference Will, Sebastian.
- [Multi angle] RNA design in theory and practice / Author of the conference Findeiss, Sven.
- [Multi angle] RNA secondary structures / Author of the conference Hofacker, Ivo.
- [Post-edited] Improving RNA secondary structure prediction / Author of the conference Lorenz, Ronny.
Bibliography
- Bernhart, S.H., Hofacker, I.L., Will, S., Gruber, A.R., & Stadler, P.F. (2008). RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics, 9(1), 13 p. - https://doi.org/10.1186/1471-2105-9-474
- Ding, Y., Chan, C.Y., & Lawrence, C.E. (2005). RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA, 11, 1157-1166 - http://dx.doi.org/10.1261/rna.2500605
- Gardner, P.P., Wilm, A., & Washietl, S. (2005). A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Research, 33(8), 2433-2439 - https://doi.org/10.1093/nar/gki541
- Heyne, S., Costa, F., Rose, D., & Backofen, R. (2012). GraphClust: alignment-free structural clustering of local RNA secondary structures. Bioinformatics, 28(12), i224-i232 - https://doi.org/10.1093/bioinformatics/bts224
- Hofacker, I.L., Bernhart, S.H.F., & Stadler, P.F. (2004). Alignment of RNA base pairing probability matrices. Bioinformatics, 20(14), 2222-2227 - https://doi.org/10.1093/bioinformatics/bth229
- Nawrocki, E.P., & Eddy, S.R. (2013). Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics, 29(22), 2933-2935 - https://doi.org/10.1093/bioinformatics/btt509
- Rivas, E., Clements, J., & Eddy, S.R. (2017). A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs. Nature Methods, 14, 45-48 - https://doi.org/10.1038/nmeth.4066
- Rivas, E., & Eddy, S.R. (2001). Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics, 2(1), 19 p. - https://doi.org/10.1186/1471-2105-2-8
- Washietl, S., Hofacker, I.L., & Stadler, P.F. (2005). Fast and reliable prediction of noncoding RNAs. Proceedings of the National Academy of Sciences of the United States of America, 102(7), 2454-2459 - https://doi.org/10.1073/pnas.0409169102
- Weinberg, Z., & Breaker, R.R. (2011). R2R - software to speed the depiction of aesthetic consensus RNA secondary structures. BMC Bioinformatics, 12(1), 9 p. - https://doi.org/10.1186/1471-2105-12-3
- Will, S., Otto, C., Miladi, M., Möhl, M., & Backofen, R. (2015). SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics. Bioinformatics, 31(15), 2489-2496 - https://doi.org/10.1093/bioinformatics/btv185
- Will, S., Joshi, T., Hofacker, I.L., Stadler, P.F., & Backofen, R. (2012). LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs. RNA, 18, 900-914 - http://dx.doi.org/10.1261/rna.029041.111
- Will, S., Reiche, K., Hofacker, I.L., Stadler, P.F., & Backofen, R. (2007). Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering. PLOS Computational Biology, 3(4), e65 - https://doi.org/10.1371/journal.pcbi.0030065
