The RNA shapes studio

Janssen S, Giegerich R (2014)
Bioinformatics 31(3): 423-425.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
URL
DOI
Autor*in
Janssen, StefanUniBi ; Giegerich, RobertUniBi
Einrichtung
Technische Fakultät
Centrum für Biotechnologie
Abstract / Bemerkung
Motivation: Abstract shape analysis, first proposed in 2004, allows one to extract several relevant structures from the folding space of an RNA sequence, preferable to focusing in a single structure of minimal free energy. We report recent extensions to this approach.Results: We have rebuilt the original RNAshapes as a repository of components that allows us to integrate several established tools for RNA structure analysis: RNAshapes, RNAalishapes and pknotsRG, including its recent extension pKiss. As a spin-off, we obtain heretofore unavailable functionality: e. g. with pKiss, we can now perform abstract shape analysis for structures holding pseudoknots up to the complexity of kissing hairpin motifs. The new tool pAliKiss can predict kissing hairpin motifs from aligned sequences. Along with the integration, the functionality of the tools was also extended in manifold ways.Availability and implementation: As before, the tool is available on the Bielefeld Bioinformatics server at http://bibiserv.cebitec.uni-bielefeld.de/rnashapesstudio.Contact: bibi-help@cebitec.uni-bielefeld.de
Erscheinungsjahr
2014
Zeitschriftentitel
Bioinformatics
Band
31
Ausgabe
3
Seite(n)
423-425
ISSN
1367-4803
eISSN
1460-2059
Page URI
https://pub.uni-bielefeld.de/record/2700599

Zitieren

Janssen S, Giegerich R. The RNA shapes studio. Bioinformatics. 2014;31(3):423-425.
Janssen, S., & Giegerich, R. (2014). The RNA shapes studio. Bioinformatics, 31(3), 423-425. doi:10.1093/bioinformatics/btu649
Janssen, Stefan, and Giegerich, Robert. 2014. “The RNA shapes studio”. Bioinformatics 31 (3): 423-425.
Janssen, S., and Giegerich, R. (2014). The RNA shapes studio. Bioinformatics 31, 423-425.
Janssen, S., & Giegerich, R., 2014. The RNA shapes studio. Bioinformatics, 31(3), p 423-425.
S. Janssen and R. Giegerich, “The RNA shapes studio”, Bioinformatics, vol. 31, 2014, pp. 423-425.
Janssen, S., Giegerich, R.: The RNA shapes studio. Bioinformatics. 31, 423-425 (2014).
Janssen, Stefan, and Giegerich, Robert. “The RNA shapes studio”. Bioinformatics 31.3 (2014): 423-425.

Link(s) zu Volltext(en)
URL
http://bioinformatics.oxfordjournals.org/content/early/2014/10/22/bioinformatics.btu649.abstract
Access Level
Restricted Closed Access

29 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Characterization of mammalian Lipocalin UTRs in silico: Predictions for their role in post-transcriptional regulation.
Mejias A, Diez-Hermano S, Ganfornina MD, Gutierrez G, Sanchez D., PLoS One 14(3), 2019
PMID: 30840684
RCPred: RNA complex prediction as a constrained maximum weight clique problem.
Legendre A, Angel E, Tahi F., BMC Bioinformatics 20(suppl 3), 2019
PMID: 30925864
tRex: A Web Portal for Exploration of tRNA-Derived Fragments in Arabidopsis thaliana.
Thompson A, Zielezinski A, Plewka P, Szymanski M, Nuc P, Szweykowska-Kulinska Z, Jarmolowski A, Karlowski WM., Plant Cell Physiol 59(1), 2018
PMID: 29145635
Bi-objective integer programming for RNA secondary structure prediction with pseudoknots.
Legendre A, Angel E, Tahi F., BMC Bioinformatics 19(1), 2018
PMID: 29334887
Design of RNAs: comparing programs for inverse RNA folding.
Churkin A, Retwitzer MD, Reinharz V, Ponty Y, Waldispühl J, Barash D., Brief Bioinform 19(2), 2018
PMID: 28049135
Inferring RNA sequence preferences for poorly studied RNA-binding proteins based on co-evolution.
Yang S, Wang J, Ng RT., BMC Bioinformatics 19(1), 2018
PMID: 29529991
A comprehensive review of web-based resources of non-coding RNAs for plant science research.
Liao P, Li S, Cui X, Zheng Y., Int J Biol Sci 14(8), 2018
PMID: 29989090
SMARTIV: combined sequence and structure de-novo motif discovery for in-vivo RNA binding data.
Polishchuk M, Paz I, Yakhini Z, Mandel-Gutfreund Y., Nucleic Acids Res 46(w1), 2018
PMID: 29800452
Challenges and approaches to predicting RNA with multiple functional structures.
Schroeder SJ., RNA 24(12), 2018
PMID: 30143552
Prediction of secondary and tertiary structures of human BC200 RNA (BCYRN1) based on experimental and bioinformatic cross-validation.
Sosińska-Zawierucha P, Zawierucha P, Bręborowicz A, Barciszewski J., Biochem J 475(17), 2018
PMID: 30072491
A planarian nidovirus expands the limits of RNA genome size.
Saberi A, Gulyaeva AA, Brubacher JL, Newmark PA, Gorbalenya AE., PLoS Pathog 14(11), 2018
PMID: 30383829
Pepo aphid-borne yellows virus: a new species in the genus Polerovirus.
Ibaba JD, Laing MD, Gubba A., Virus Genes 53(1), 2017
PMID: 27623838
Bioinformatic tools for analysis of CLIP ribonucleoprotein data.
De S, Gorospe M., Wiley Interdiscip Rev RNA 8(4), 2017
PMID: 28008714
Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs.
Lim CS, Brown CM., Front Microbiol 8(), 2017
PMID: 29354101
Search for 5'-leader regulatory RNA structures based on gene annotation aided by the RiboGap database.
Naghdi MR, Smail K, Wang JX, Wade F, Breaker RR, Perreault J., Methods 117(), 2017
PMID: 28279853
RNAblueprint: flexible multiple target nucleic acid sequence design.
Hammer S, Tschiatschek B, Flamm C, Hofacker IL, Findeiß S., Bioinformatics 33(18), 2017
PMID: 28449031
RNA inverse folding using Monte Carlo tree search.
Yang X, Yoshizoe K, Taneda A, Tsuda K., BMC Bioinformatics 18(1), 2017
PMID: 29110632
Initiation on the divergent Type I cadicivirus IRES: factor requirements and interactions with the translation apparatus.
Asnani M, Pestova TV, Hellen CU., Nucleic Acids Res 44(7), 2016
PMID: 26873921
Guidelines for the optimal design of miRNA-based shRNAs.
Bofill-De Ros X, Gu S., Methods 103(), 2016
PMID: 27083402
RCK: accurate and efficient inference of sequence- and structure-based protein-RNA binding models from RNAcompete data.
Orenstein Y, Wang Y, Berger B., Bioinformatics 32(12), 2016
PMID: 27307637
SwiSpot: modeling riboswitches by spotting out switching sequences.
Barsacchi M, Novoa EM, Novoa EM, Kellis M, Bechini A., Bioinformatics 32(21), 2016
PMID: 27378291
An Adaptive Defect Weighted Sampling Algorithm to Design Pseudoknotted RNA Secondary Structures.
Zandi K, Butler G, Kharma N., Front Genet 7(), 2016
PMID: 27499762
Accurate Classification of RNA Structures Using Topological Fingerprints.
Huang J, Li K, Gribskov M., PLoS One 11(10), 2016
PMID: 27755571
Widespread distribution and structural diversity of Type IV IRESs in members of Picornaviridae.
Asnani M, Kumar P, Hellen CU., Virology 478(), 2015
PMID: 25726971
Dietary MicroRNA Database (DMD): An Archive Database and Analytic Tool for Food-Borne microRNAs.
Chiang K, Shu J, Zempleni J, Cui J., PLoS One 10(6), 2015
PMID: 26030752
Characterisation of aptamer-target interactions by branched selection and high-throughput sequencing of SELEX pools.
Dupont DM, Larsen N, Jensen JK, Andreasen PA, Kjems J., Nucleic Acids Res 43(21), 2015
PMID: 26163061
Molecular and Functional Characterization of ssDNA Aptamers that Specifically Bind Leishmania infantum PABP.
Guerra-Pérez N, Ramos E, García-Hernández M, Pinto C, Soto M, Martín ME, González VM., PLoS One 10(10), 2015
PMID: 26457419
Coevolution Pattern and Functional Conservation or Divergence of miR167s and their targets across Diverse Plant Species.
Barik S, Kumar A, Sarkar Das S, Yadav S, Gautam V, Singh A, Singh S, Sarkar AK., Sci Rep 5(), 2015
PMID: 26459056
antaRNA--Multi-objective inverse folding of pseudoknot RNA using ant-colony optimization.
Kleinkauf R, Houwaart T, Backofen R, Mann M., BMC Bioinformatics 16(), 2015
PMID: 26581440

19 References

Daten bereitgestellt von Europe PubMed Central.

Programmed ribosomal frameshifting in decoding the SARS-CoV genome.
Baranov PV, Henderson CM, Anderson CB, Gesteland RF, Atkins JF, Howard MT., Virology 332(2), 2005
PMID: 15680415
RNAalifold: improved consensus structure prediction for RNA alignments.
Bernhart SH, Hofacker IL, Will S, Gruber AR, Stadler PF., BMC Bioinformatics 9(), 2008
PMID: 19014431
Rfam 11.0: 10 years of RNA families.
Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A., Nucleic Acids Res. 41(Database issue), 2012
PMID: 23125362
VARNA: Interactive drawing and editing of the RNA secondary structure.
Darty K, Denise A, Ponty Y., Bioinformatics 25(15), 2009
PMID: 19398448
A discipline of dynamic programming over sequence data
Giegerich R., 2004
Abstract shapes of RNA.
Giegerich R, Voss B, Rehmsmeier M., Nucleic Acids Res. 32(16), 2004
PMID: 15371549
Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction.
Janssen S, Schudoma C, Steger G, Giegerich R., BMC Bioinformatics 12(), 2011
PMID: 22051375
ViennaRNA Package 2.0.
Lorenz R, Bernhart SH, Honer Zu Siederdissen C, Tafer H, Flamm C, Stadler PF, Hofacker IL., Algorithms Mol Biol 6(), 2011
PMID: 22115189
Improved RNA secondary structure prediction by maximizing expected pair accuracy.
Lu ZJ, Gloor JW, Mathews DH., RNA 15(10), 2009
PMID: 19703939
Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics.
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
Locomotif: from graphical motif description to RNA motif search.
Reeder J, Reeder J, Giegerich R., Bioinformatics 23(13), 2007
PMID: 17646322
Conservation and Occurrence of Trans-Encoded sRNAs in the Rhizobiales.
Reinkensmeier J, Schluter JP, Giegerich R, Becker A., Genes (Basel) 2(4), 2011
PMID: 24710299
Bellman's GAP--a language and compiler for dynamic programming in sequence analysis.
Sauthoff G, Mohl M, Janssen S, Giegerich R., Bioinformatics 29(5), 2013
PMID: 23355290
Versatile and declarative dynamic programming using pair algebras.
Steffen P, Giegerich R., BMC Bioinformatics 6(), 2005
PMID: 16156887
KnotInFrame: prediction of -1 ribosomal frameshift events.
Theis C, Reeder J, Giegerich R., Nucleic Acids Res. 36(18), 2008
PMID: 18820303
Prediction of RNA secondary structure including kissing hairpin motifs
Theis C., 2010
Structural analysis of aligned RNAs.
Voss B., Nucleic Acids Res. 34(19), 2006
PMID: 17020924
Complete probabilistic analysis of RNA shapes.
Voss B, Giegerich R, Rehmsmeier M., BMC Biol. 4(), 2006
PMID: 16480488
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 25273103
PubMed | Europe PMC

Suchen in

Google Scholar