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RapidShapes specifications


Unique identifier OMICS_27186
Name RapidShapes
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Stefan Janssen

Publication for RapidShapes


The RNA shapes studio

2015 Bioinformatics
PMCID: 4308662
PMID: 25273103
DOI: 10.1093/bioinformatics/btu649

RapidShapes citations


Molecular and Functional Characterization of ssDNA Aptamers that Specifically Bind Leishmania infantum PABP

PLoS One
PMCID: 4601788
PMID: 26457419
DOI: 10.1371/journal.pone.0140048

[…] To proceed to their structural characterization, the sequences of ApPABP#3, ApPABP#7 and ApPABP#11 were analyzed using the program Rapidshape (http://bibiserv.techfak.uni-bielefeld.de/rapidshapes/) [] and the potential most stable secondary structures for each aptamer in the same condition that those used during selection are shown in . Secondary structure prediction indicates that […]


Thermodynamic matchers for the construction of the cuckoo RNA family

RNA Biol
PMCID: 4615179
PMID: 25779873
DOI: 10.1080/15476286.2015.1017206
call_split See protocol

[…] r, possibly modifying its design several times and debugging the implemented dynamic programming algorithm, would be prohibitive in practice. Fortunately, there is some automated support. The program RapidShapes generates TDMs from abstract shape specifications, such as "[[][][]]" for the cloverleaf shape. This allows one to directly compute this shape's contribution to the partition function of x […]


Identification and profiling of miRNAs during herbivory reveals jasmonate dependent and independent patterns of accumulation in Nicotiana attenuata

BMC Plant Biol
PMCID: 3502350
PMID: 23134682
DOI: 10.1186/1471-2229-12-209
call_split See protocol

[…] C) and ionic conditions (1M NaCl) with minimum free energy (MFE) formations (Table‚ÄČ ). Predicted miRNA-precursors were additionally depicted using RNAshapes ( http://bibiserv.techfak.uni-bielefeld.de/rapidshapes) [] to create stem-and-loop structures ( Additional file ). For TAS3 identification we used the following TAS3 orthologs: Saccharum officinarum (EU327139), Sorghum bicolor (EU327137), Zea […]


Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction

BMC Bioinformatics
PMCID: 3293930
PMID: 22051375
DOI: 10.1186/1471-2105-12-429

[…] nces. Therefore, we conclude Conclusion 5 A strategy to efficiently compute level-2 shapes for long sequences is desirable Let us sketch a strategy how this can be achieved, borrowing ideas from the RAPIDSHAPES method []. Directly accessing the complete level-2 shape space of a long sequence appears infeasible. But we can compute a level-5 analysis at 90% or 100% coverage quickly, by reporting a […]


Faster computation of exact RNA shape probabilities

PMCID: 2828121
PMID: 20080511
DOI: 10.1093/bioinformatics/btq014
call_split See protocol

[…] A TDM folds a sequence only to a restricted set of structures. For RapidShapes, such a restricted set of structures comprises all structures of a particular shape (and no other). A TDM can compute the partition function value Qp(s) of its restricted folding space Fp( […]


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RapidShapes institution(s)
Practical Computer Science, Faculty of Technology, Bielefeld University, Bielefeld, Germany

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