SARSE 1.37 – RNA Sequence Editor

SARSE 1.37

:: DESCRIPTION

SARSE (semiautomated RNA sequence editor) is a graphical sequence editor for working with structural alignments of RNA.

::DEVELOPER

E. S. Andersen, A. Lind-Thomsen and J. Gorodkin

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 SARSE

:: MORE INFORMATION

Citation:

Semiautomated improvement of RNA alignments
E. S. Andersen, A. Lind-Thomsen, B. Knudsen, S. E. Kristensen, J. H. Havgaard, E. Torarinsson, N. Larsen, C. Zwieb, P. Sestoft, J. Kjems and J. Gorodkin,
RNA 13:1850-1859, 2007.

NOFOLD 1.0.1 – RNA Structure Clustering without Folding or Alignment

NOFOLD 1.0.1

:: DESCRIPTION

NoFold is an approach for characterizing and clustering RNA secondary structures without computational folding or alignment. It works by mapping each RNA sequence of interest to a structural feature space, where each coordinate within the space corresponds to the probabilistic similarity of the sequence to an empirically defined structure model (e.g. Rfam family covariance models).

::DEVELOPER

the Kim Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • R

:: DOWNLOAD

NOFOLD

:: MORE INFORMATION

Citation

Middleton SA, Kim J.
NoFold: RNA structure clustering without folding or alignment.
RNA. 2014 Nov;20(11):1671-83. doi: 10.1261/rna.041913.113. Epub 2014 Sep 18. PMID: 25234928; PMCID: PMC4201820.

XRNA 2.0 – Creation, Annotation & Display of RNA Secondary Structure Diagrams

XRNA 2.0

:: DESCRIPTION

XRNA is a Java based suite of tools for the creation, annotation and display of RNA secondary structure diagrams.XRNA provides editing tools for easy modification of publication quality secondary diagrams that can be either drawn manually, or through automatic generation. Other features include grouping, numbering and structure annotation. XRNA secondary structures may be saved in a native format, or exported as postscript for printing and further manipulation in programs such as Adobe Illustrator.

::DEVELOPER

RNA Center, UCSC

:: SCREENSHOTS


:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Perl

:: DOWNLOAD

XRNA

:: MORE INFORMATION

ViennaRNA 2.5.0 – RNA Secondary Structure Prediction & Comparison

ViennaRNA 2.5.0

:: DESCRIPTION

ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.

Vienna RNA WebServers

::DEVELOPER

Theoretical Biochemistry Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Mac OsX/ Windows

:: DOWNLOAD

Vienna RNA

:: MORE INFORMATION

Citation

Methods Mol Biol. 2015;1269:307-26. doi: 10.1007/978-1-4939-2291-8_19.
The ViennaRNA web services.
Gruber AR1, Bernhart SH, Lorenz R.

Ivo L. Hofacker
Vienna RNA secondary structure serverNucl.
Acids Res. (2003) 31 (13): 3429-3431

Lorenz, Ronny and Bernhart, Stephan H. and Höner zu Siederdissen, Christian and Tafer, Hakim and Flamm, Christoph and Stadler, Peter F. and Hofacker, Ivo L.
ViennaRNA Package 2.0
Algorithms for Molecular Biology, 6:1 26, 2011, doi:10.1186/1748-7188-6-26

RNAmigos – RNA Small Molecule Ligand Prediction

RNAmigos

:: DESCRIPTION

RNAmigos is a Graph Neural Network for predicting RNA small molecule ligands.

::DEVELOPER

Carlos Oliver

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

RNAmigos

:: MORE INFORMATION

Citation:

Oliver C, Mallet V, Gendron RS, Reinharz V, Hamilton WL, Moitessier N, Waldispühl J.
Augmented base pairing networks encode RNA-small molecule binding preferences.
Nucleic Acids Res. 2020 Aug 20;48(14):7690-7699. doi: 10.1093/nar/gkaa583. PMID: 32652015; PMCID: PMC7430648.

VeRNAl – Discovering Flexible Motifs in RNA Graphs

VeRNAl

:: DESCRIPTION

veRNAl is an algorithm for identifying fuzzy recurrent subgraphs in RNA 3D networks.

::DEVELOPER

Carlos Oliver

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

VeRNAl

:: MORE INFORMATION

Citation:

Oliver C, Mallet V, Philippopoulos P, Hamilton WL, Waldispühl J.
VeRNAl: A Tool for Mining Fuzzy Network Motifs in RNA.
Bioinformatics. 2021 Nov 15:btab768. doi: 10.1093/bioinformatics/btab768. Epub ahead of print. PMID: 34791045.

SimRNA 3.20 – Simulations of RNA Conformational Dynamics

SimRNA 3.20

:: DESCRIPTION

SimRNA is a tool for simulations of RNA conformational dynamics (folding, unfolding, multiple chain complex formation etc.), and its applications include RNA 3D structure prediction.

::DEVELOPER

Bujnicki lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 SimRNA

:: MORE INFORMATION

Citation

Boniecki MJ, Lach G, Dawson WK, Tomala K, Lukasz P, Soltysinski T, Rother KM, Bujnicki JM.
SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction.
Nucleic Acids Res. 2016 Apr 20;44(7):e63. doi: 10.1093/nar/gkv1479. Epub 2015 Dec 19. PMID: 26687716; PMCID: PMC4838351.

ModeRNA 1.7.1 – Comparative RNA 3D Modeling

ModeRNA 1.7.1

:: DESCRIPTION

ModeRNA is a program for comparative modeling of RNA 3D structures. It requires a pairwise sequence alignment and a structural template to generate a 3D structural model of the target RNA sequence via either a fully automated or script-based approaches. ModeRNA is capable of handling 115 different nucleotide modifications and bridging gaps using fragments derived from an extensive fragment library.

::DEVELOPER

Bujnicki Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

ModeRNA

:: MORE INFORMATION

Citation

Magdalena Rother, Kristian Rother, Tomasz Puton and Janusz M. Bujnicki
ModeRNA: a tool for comparative modeling of RNA 3D structure
Nucl. Acids Res.(2011)doi: 10.1093

RNA-Pareto 20130814 – Interactive Analysis of Pareto-optimal RNA Sequence-Structure Alignments

RNA-Pareto 20130814

:: DESCRIPTION

RNA-Pareto is a software for structural RNA alignment by multi-objective optimization.

::DEVELOPER

Medical Systems Biology, University of Ulm

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/MacOsX/Linux
  • Java
:: DOWNLOAD

 RNA-Pareto

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Dec 1;29(23):3102-4. doi: 10.1093/bioinformatics/btt536. Epub 2013 Sep 16.
RNA-Pareto: interactive analysis of Pareto-optimal RNA sequence-structure alignments.
Schnattinger T1, Schöning U, Marchfelder A, Kestler HA.

FRUUT 2.46 – Fast RNA Unrooted Unordered Tree Alignment

FRUUT 2.46

:: DESCRIPTION

FRUUT computes an RNA structure alignment of two given RNA molecules. We generalize previous algorithms that either solved the problem in an asymmetric manner, or were restricted to the rooted and/or ordered cases. Focusing here on the most general unrooted unordered case, we show that our algorithm has an O(nTnS min(dT, dS)) time complexity, where nT and nS are the number of nodes and dT and dS are the maximum node degrees in the input trees T and S, respectively. This maintains (and slightly improves) the time complexity of previous, less general algorithms for the problem.

::DEVELOPER

Michal Ziv-Ukelson’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac / Windows
  • Java

:: DOWNLOAD

 FRUUT

:: MORE INFORMATION

Citation

Algorithms Mol Biol. 2013 Apr 16;8(1):13. doi: 10.1186/1748-7188-8-13.
Unrooted unordered homeomorphic subtree alignment of RNA trees.
Milo N1, Zakov S, Katzenelson E, Bachmat E, Dinitz Y, Ziv-Ukelson M.

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