get_size_NN v1 – Neutral Network Size Estimation

get_size_NN v1

:: DESCRIPTION

get_size_NN calculates, via nested Monte Carlo, an estimate of the size of the neutral set (network) of a given RNA secondary structure.

::DEVELOPER

Andreas Wagner Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 get_size_NN

:: MORE INFORMATION

Citation:

Thomas Jörg, Olivier C Martin and Andreas Wagner
Neutral network sizes of biological RNA molecules can be computed and are atypically large.
BMC Bioinformatics 2008, 9:464

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

Scirpy v0.10.1 – Scanpy Extension for analyzing Single-cell T-cell Receptor-sequencing data

Scirpy v0.10.1

:: DESCRIPTION

Scirpy is a scalable python-toolkit to analyse T cell receptor (TCR) or B cell receptor (BCR) repertoires from single-cell RNA sequencing (scRNA-seq) data. It seamlessly integrates with the popular scanpy library and provides various modules for data import, analysis and visualization.

::DEVELOPER

the Institute of Bioinformatics, Innsbruck Medical University

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

Scirpy

:: MORE INFORMATION

Citation

Sturm G, Szabo T, Fotakis G, Haider M, Rieder D, Trajanoski Z, Finotello F.
Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data.
Bioinformatics. 2020 Sep 15;36(18):4817-4818. doi: 10.1093/bioinformatics/btaa611. PMID: 32614448; PMCID: PMC7751015.

meRanTK 1.2.1b – Methylated RNA Analysis ToolKit

meRanTK 1.2.1b

:: DESCRIPTION

meRanTK is a versatile high performance toolkit for complete analysis of methylated RNA data.

::DEVELOPER

the Institute of Bioinformatics, Innsbruck Medical University

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 meRanTK

:: MORE INFORMATION

Citation

meRanTK: methylated RNA analysis ToolKit.
Rieder D, Amort T, Kugler E, Lusser A, Trajanoski Z.
Bioinformatics. 2015 Nov 4. pii: btv647.

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.

incaRNAfbinv / RNAfbinv 2.0 – Fragment-based design of RNA sequences

incaRNAfbinv / RNAfbinv 2.0

:: DESCRIPTION

incaRNAfbinv is a web server which implements the method devised in RNAfbinv and offers an interactive environment for the inverse folding of RNA using a fragment-based design approach. It takes as input: a target RNA secondary structure; optional sequence and motif constraints; optional target minimum free energy, neutrality and GC content. In addition to the design of synthetic regulatory sequences, it can be used as a pre-processing step for the detection of novel natural occurring RNAs.

RNAfbinv is a fragment based RNA design tool. It uses a simulated annealing process to optimize a 2D RNA structure.

::DEVELOPER

incaRNAfbinv team

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

RNAfbinv

:: MORE INFORMATION

Citation

Retwitzer MD, Reinharz V, Churkin A, Ponty Y, Waldispühl J, Barash D.
incaRNAfbinv 2.0: a webserver and software with motif control for fragment-based design of RNAs.
Bioinformatics. 2020 May 1;36(9):2920-2922. doi: 10.1093/bioinformatics/btaa039. PMID: 31971575.

incaRNAfbinv: a web server for the fragment-based design of RNA sequences.
Drory Retwitzer M, Reinharz V, Ponty Y, Waldispühl J, Barash D.
Nucleic Acids Res. 2016 Jul 8;44(W1):W308-14. doi: 10.1093/nar/gkw440. Epub 2016 May 16.

Bioinformatics. 2013 Nov 15;29(22):2938-40. doi: 10.1093/bioinformatics/btt494. Epub 2013 Aug 23.
RNAfbinv: an interactive Java application for fragment-based design of RNA sequences.
Weinbrand L1, Avihoo A, Barash D.

RNAMoIP 1.1 – Automated Prediction Framework for RNA Tertiary Structures

RNAMoIP 1.1

:: DESCRIPTION

RNA-MoIP is an integer programming framework that refines predicted secondary structures (i.e. removes incorrect canonical base-pairs) to accommodate the insertion of RNA 3D motifs (i.e. hairpins, internal loops and k-way junctions). The predictions can be used as templates to generate complete 3D structures with the MC-Sym program.

::DEVELOPER

Computer Science and Biology at McGill

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 RNAMoIP

:: MORE INFORMATION

Citation:

Yao J, Reinharz V, Major F, Waldispühl J.
RNA-MoIP: prediction of RNA secondary structure and local 3D motifs from sequence data.
Nucleic Acids Res. 2017 Jul 3;45(W1):W440-W444. doi: 10.1093/nar/gkx429. Erratum in: Nucleic Acids Res. 2017 Jul 3;45(W1):W573. PMID: 28525607; PMCID: PMC5793723.

RNAmap2D 1.7.5 – Visualization of 2D maps of RNA Structures

RNAmap2D 1.7.5

:: DESCRIPTION

RNAMAP2D is a software to the analysis of contact maps of RNA structures and protein – RNA complexes. The program deals with modified base pairs which are very frequent in RNA and includes ligands and ions which plays key roles in forming and stabilizing RNA structures. What is more, it is possible to show on the computed map whether some of the identified contacts are recognized as belonging to one of the 12 base pairs families, are canonical Watson – Crick pairs, or are 4 classes of stacking interactions. The overlap of the 2D maps of two structures can be easily calculated, providing a measure of RNA structure similarity.

::DEVELOPER

Bujnicki Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

  RNAmap2D

:: MORE INFORMATION

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.