2016
DOI: 10.1093/nar/gkw440
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incaRNAfbinv: a web server for the fragment-based design of RNA sequences

Abstract: In recent years, new methods for computational RNA design have been developed and applied to various problems in synthetic biology and nanotechnology. Lately, there is considerable interest in incorporating essential biological information when solving the inverse RNA folding problem. Correspondingly, aims at including biologically meaningful constraints and is the only program to-date that performs a fragment-based design of RNA sequences. In doing so it allows the design of sequences that do not necessarily… Show more

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Cited by 15 publications
(12 citation statements)
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“…The above comparison is by no means exhaustive and can be supplemented by the additional references [ 43–45 , 52 ]. These references could benefit a reader interested in the topic of runtime comparisons, design capabilities and properties of the output sequences produced by each method.…”
Section: Discussionmentioning
confidence: 99%
See 2 more Smart Citations
“…The above comparison is by no means exhaustive and can be supplemented by the additional references [ 43–45 , 52 ]. These references could benefit a reader interested in the topic of runtime comparisons, design capabilities and properties of the output sequences produced by each method.…”
Section: Discussionmentioning
confidence: 99%
“…IncaRNAfbinv [ 52 ] is a recent program for fragment-based design. It is available as a Web server at https://www.cs.bgu.ac.il/incaRNAfbinv/ .…”
Section: Details Of Usementioning
confidence: 99%
See 1 more Smart Citation
“…Most RNA design algorithms are based on the heuristic approach. Some of the well-known RNA design packages are RNA-SSD [7] and INFO-RNA [8] using local stochastic searches, RNA-ensign [9] and improved version of RNAensign called IncaRNAtion [10] to decrease time complexity using global sampling methodology, MODENA [11], Frnakestein [12], GGI-FOLD [13], ERD [14] and our algorithm SIMARD [6] using evolutionary algorithms, incaR-NAfbinv [15] using fragment-based design, and lastly an-taRNA [16] which uses the ant colony optimization technique. Recently, some researchers has developed an online game to help with the RNA design problem [17].…”
Section: A Computational Intelligence For Rna Prediction and Designmentioning
confidence: 99%
“…AntaRNA employs both IUPAC format sequence and GC-content constraints to find the best sequence for a given structure using ant colony optimization (Kleinkauf et al, 2015). IncaRNAfbinv (Retwitzer et al, 2016) merges incaRNAtion (Reinharz et al, 2013) with RNAfbinv (Weinbrand et al, 2013) to solve the RD problem based on biologically meaningful constraints. RNAexinv (Avihoo et al, 2011) predicts a sequence for a given structure from shape representation and physical attributes.…”
Section: Introductionmentioning
confidence: 99%