ParaRNA 1.0 – Computing Parametric Alignment of Two RNA Structures

ParaRNA 1.0

:: DESCRIPTION

ParaRNAis a software for computing parametric alignment of two RNA structures. It takes two RNA secondary structures and match score, indel score, the range of mismatch score and the range of gap score as its input, and computes all the optimal alignments in the parametric space given by mismatch score and gap score, and show them in a graphic interface.

::DEVELOPER

Lusheng Wang

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 ParaRNA

:: MORE INFORMATION

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

do_x3dna 2018 – Analyze Fluctuations in DNA or RNA Structures in Molecular Dynamics Trajectories

do_x3dna 2018

:: DESCRIPTION

The do_x3dna package has been developed to analyze the structural fluctuations of DNA or RNA during molecular dynamics simulations.

::DEVELOPER

Rajendra Kumar

:: SCREENSHOTS

N/a

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX
  • 3DNA

:: DOWNLOAD

 do_x3dna

:: MORE INFORMATION

Citation

do_x3dna: A tool to analyze structural fluctuations of dsDNA or dsRNA from molecular dynamics simulations.
Kumar R, Grubmüller H.
Bioinformatics. 2015 Apr 2. pii: btv190.

ernwin 1.0.1 – RNA Structure Prediction

ernwin 1.0.1

:: DESCRIPTION

ernwin is a program for sampling coarse grain 3D RNA structures.

::DEVELOPER

Peter Kerpedjiev

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • Python

:: DOWNLOAD

 ernwin

:: MORE INFORMATION

Citation:

Predicting RNA 3D structure using a coarse-grain helix-centered model.
Kerpedjiev P, Höner Zu Siederdissen C, Hofacker IL.
RNA. 2015 Jun;21(6):1110-21. doi: 10.1261/rna.047522.114.

RSmatch 2.0 – Comparison of RNA structures

RSmatch 2.0

:: DESCRIPTION

RSmatch is a package for comparing RNA structures via 1) pair-wise and DB searches; 2) multiple structure alignment with common structure computation; 3)iterative DB searches.

::DEVELOPER

Shapiro Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

RSmatch

Khaladkar M, Bellofatto V, Wang JT, Tian B, Shapiro BA.
RADAR: a web server for RNA data analysis and research.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W300-4. doi: 10.1093/nar/gkm253. Epub 2007 May 21. PMID: 17517784; PMCID: PMC1933136.

Vfold 2.0 – RNA Structure and Folding Thermodynamics Prediction

Vfold 2.0

:: DESCRIPTION

Vfold is a software package to evaluate the stable structures and the folding free energies for RNA secondary structures and pseudoknotted structures. Recently, the Vfold model has been extended to predict loop-stem tertiary interactions in RNA pseudoknots

::DEVELOPER

Shi-Jie Chen Research Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 Vfold

:: MORE INFORMATION

Citation

Vfold: a web server for RNA structure and folding thermodynamics prediction.
Xu X, Zhao P, Chen SJ.
PLoS One. 2014 Sep 12;9(9):e107504. doi: 10.1371/journal.pone.0107504. eCollection 2014.

PRI-Modeler 1.3 – Extract RNA Structure elements from PDB files of Protein-RNA Complexes

PRI-Modeler 1.3

:: DESCRIPTION

PRI-Modeler (protein-RNA interaction modeler)analyzes the conformation of the RNA, calculates the hydrogen bond (H bond) and van der Waals interactions between amino acids and nucleotides, extracts secondary and tertiary RNA structure elements, and identifies the patterns of interactions between the proteins and RNAs. This paper presents PRI-Modeler and its application to the hydrogen bond and van der Waals interactions in the most representative set of protein-RNA complexes. The analysis reveals several interesting interaction patterns at various levels.

::DEVELOPER

Biocomputing Lab. School of Computer Science and Engineering Inha University, Inchon

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

PRI-Modeler

:: MORE INFORMATION

Citation

Kyungsook Han, Chirag Nepa
PRI-Modeler: Extracting RNA structural elements from PDB files of protein–RNA complexes
FEBS Lett. 2007 May 1;581(9):1881-90.

Gardenia – Compare & Align RNA Structures

Gardenia

:: DESCRIPTION

Gardenia is a program that Compares & aligns RNA secondary structures,without pseudoknots. The resulting alignment takes into account both the primary structure and the secondary structure.

::DEVELOPER

Bonsai Bioinformatics – INRIA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  Linux / MacOsX
  • C Complier

:: DOWNLOAD

Gardenia

:: MORE INFORMATION

Citation

Guillaume Blin, Alain Denise, Serge Dulucq, Claire Herrbach, Helene Touzet
Alignment of RNA structures
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2008

RNAsnp 1.2 – Identifying local RNA Structures Disrupted by SNPs

RNAsnp 1.2

:: DESCRIPTION

RNAsnp is a software for efficient detection of local RNA secondary structure changes induced by SNPs

::DEVELOPER

Center for non-coding RNA in Technology and Health (RTH)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  RNAsnp

:: MORE INFORMATION

Citation:

Hum Mutat. 2013 Apr;34(4):546-56. doi: 10.1002/humu.22273.
RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs.
Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, Gorodkin J.

SAVoR – Sequencing Annotation and Visualization of RNA structures

SAVoR

:: DESCRIPTION

SAVoR is an easy-to-use web application that allows the user to visualize RNA-seq data and other genomic annotations on RNA secondary structures. SAVoR is designed to help researchers visualize sequencing data in the context of RNA secondary structures.

::DEVELOPER

 Wang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

SAVoR: a server for sequencing annotation and visualization of RNA structures.
Li F, Ryvkin P, Childress DM, Valladares O, Gregory BD, Wang LS.
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W59-64. doi: 10.1093/nar/gks310.