Assemble2 2.3 – Construct & Study RNA Architectures

Assemble2 2.3

:: DESCRIPTION

Assemble proposes an intuitive graphical interface to study and construct complex three-dimensional RNA structures. When an RNA tertiary structure is opened with Assemble, it is automatically annotated with a secondary structure definition. This secondary structure can be used as a map to analyze the original tertiary structure. Using a secondary structure definition, Assemble can also produce a first draft of a 3D Model. Then the construction process can be pursued “by hand” using several widgets.

::DEVELOPER

Dr. Fabrice Jossinet at the laboratory of Pr. Eric Westhof

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

Assemble

:: MORE INFORMATION

Citation

Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels
Fabrice Jossinet; Thomas E Ludwig; Eric Westhof
Bioinformatics 2010; doi: 10.1093/bioinformatics/btq321

MIMEAnTo – Profiling functional RNA in Mutational Interference Mapping Experiments

MIMEAnTo

:: DESCRIPTION

Quantitative effects of each mutation at each position in the RNA can be recovered with statistical certainty using the herein developed user-friendly, cross-platform software MIMEAnTo (MIME Analysis Tool).

::DEVELOPER

MIMEAnTo team

:: SCREENSHOTS

MIMEAnTo

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Gnuplot

:: DOWNLOAD

 MIMEAnTo

:: MORE INFORMATION

Citation:

MIMEAnTo – Profiling functional RNA in Mutational Interference Mapping Experiments.
Smith MR, Smyth RP, Marquet R, von Kleist M.
Bioinformatics. 2016 Jul 10. pii: btw479.

RNAgraphdist 1.0 – Calculation of Graph-distance Distribution of the Boltzmann ensemble of RNA Secondary Structures

RNAgraphdist 1.0

:: DESCRIPTION

The RNAgraphdist calculates the equilibrium distribution of graph-distances between arbitrary pair of nucleotides in an RNA molecule. The program reads RNA structures generated from RNAsubopt, calculates their equilibrium distribution and outputs the graph-distances in a tab delimited list or in the terminal.

::DEVELOPER

RNA Bioinformatics and High Throughput Analysis Jena

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RNAgraphdist

:: MORE INFORMATION

Citation

Algorithms Mol Biol. 2014 Sep 11;9:19. doi: 10.1186/1748-7188-9-19. eCollection 2014.
Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures.
Qin J, Fricke M, Marz M, Stadler PF, Backofen R.

JAR3D – Predicting RNA 3D Motifs in Sequences

JAR3D

:: DESCRIPTION

JAR3D scores RNA hairpin and internal loop sequences against motif groups from the RNA 3D Motif Atlas, by exact sequence match for sequences already observed in 3D and by probabilistic scoring and edit distance for novel sequences.

::DEVELOPER

BGSU RNA Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs.
Roll J, Zirbel CL, Sweeney B, Petrov AI, Leontis N.
Nucleic Acids Res. 2016 May 27. pii: gkw453

Identifying novel sequence variants of RNA 3D motifs,
Craig L. Zirbel, James Roll, Blake A. Sweeney, Anton I. Petrov, Meg Pirrung, and Neocles Leontis.
Nucleic Acids Res. 2015 Sep 3;43(15):7504-20. doi: 10.1093/nar/gkv651

ViralNet – Computing Network Structures in RNA Viral Populations

ViralNet

:: DESCRIPTION

ViralNet is an application for estimating reticulated structures of mixed viral populations.

::DEVELOPER

The UEA Computational Biology Laboratory at the University of East Anglia (UEA)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 ViralNet

:: MORE INFORMATION

Citation

Inferring the Clonal Structure of Viral Populations from Time Series Sequencing
Donatien Fotso-Chedom, Pablo R. Murcia, Chris D. Greenman
arXiv:1407.7997

RNArobo 2.1.0 – RNA Structural Motif Search tool

RNArobo 2.1.0

:: DESCRIPTION

RNArobo is an RNA structural motif search tool. RNArobo can search sequence databases in FASTA format for a motif defined by a descriptor, which can specify primary and secondary structure constraints.

:: DEVELOPER

Computational Biology @ Comenius University in Bratislava

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 RNArobo

:: MORE INFORMATION

Citation

RNA motif search with data-driven element ordering.
Rampášek L, Jimenez RM, Lupták A, Vinař T, Brejová B.
BMC Bioinformatics. 2016 May 18;17(1):216. doi: 10.1186/s12859-016-1074-x.

rMAPS v1.0.1 – RNA Map analysis and Plotting server for alternative Exon Regulation

rMAPS v1.0.1

:: DESCRIPTION

rMAPS (rna Map Analysis and Plotting Server) is a web server that systematically generates RNA-maps for the analysis of RNA-binding proteins (RBPs) binding sites which have position-dependent functions.

::DEVELOPER

rMAPS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

rMAPS: RNA map analysis and plotting server for alternative exon regulation.
Park JW, Jung S, Rouchka EC, Tseng YT, Xing Y.
Nucleic Acids Res. 2016 May 12. pii: gkw410.

TfReg 3.0 – Calculating DNA or RNA Melting Temperatures and Average Strand Openings

TfReg 3.0

:: DESCRIPTION

TfReg implements the calculation of Peyrard-Bishop style Hamiltonians to obtain some physical properties of DNA and RNA duplexes. The method uses the transfer matrix technique for the calculation of the classical partition function. Also, TfReg calculates the regression of experimental versus predicted melting temperatures using the equivalent melting index.

::DEVELOPER

Gerald Weber

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 TfReg

:: MORE INFORMATION

Citation

Bioinformatics. 2013 May 15;29(10):1345-7. doi: 10.1093/bioinformatics/btt133. Epub 2013 Mar 16.
TfReg: calculating DNA and RNA melting temperatures and opening profiles with mesoscopic models.
Weber G.

RME 1.1 – RNA Secondary Structure Prediction incorporating Experimental Constraints

RME 1.1

:: DESCRIPTION

RME predict RNA secondary structure by integrating the free energy model with probing data (SHAPE, PARS, DMS).

::DEVELOPER

Lu Lab, School of Life Sciences, Tsinghua University, China

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RME

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2015 Sep 3;43(15):7247-59. doi: 10.1093/nar/gkv706. Epub 2015 Jul 13.
Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data.
Wu Y, Shi B, Ding X, Liu T, Hu X, Yip KY, Yang ZR, Mathews DH, Lu ZJ

RNAex – RNA Secondary Structure Prediction Server

RNAex

:: DESCRIPTION

RNAex is an RNA secondary structure prediction enhanced by high-throughput experimental data

::DEVELOPER

Lu Lab, School of Life Sciences, Tsinghua University, China

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

RNAex: an RNA secondary structure prediction server enhanced by high-throughput structure-probing data.
Wu Y, Qu R, Huang Y, Shi B, Liu M, Li Y, Lu ZJ.
Nucleic Acids Res. 2016 May 2. pii: gkw362.