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

varLD 1.0 – Comparison of Variation in Linkage Disequilibrium between Population

varLD 1.0

:: DESCRIPTION

varLD can be used to perform inter-population comparison of regional patterns of linkage disequilibrium (LD), and quantifies which genomic regions carry dissimilar patterns of LD across the populations compared.

::DEVELOPER

Saw Swee Hock School of Public Health

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsXR package
  • Java

:: DOWNLOAD

  varLD

:: MORE INFORMATION

Citation:

varLD: a program for quantifying variation in linkage disequilibrium patterns between populations.
Ong RT, Teo YY.
Bioinformatics. 2010 May 1;26(9):1269-70. doi: 10.1093/bioinformatics/btq125. Epub 2010 Mar 22.

clinker v0.0.23 – Gene Cluster Comparison Figure Generator

clinker v0.0.23

:: DESCRIPTION

clinker is a pipeline for easily generating publication-quality gene cluster comparison figures.

::DEVELOPER

Chooi Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Python

:: DOWNLOAD

clinker

:: MORE INFORMATION

Citation

Gilchrist CLM, Chooi YH.
Clinker & clustermap.js: Automatic generation of gene cluster comparison figures.
Bioinformatics. 2021 Jan 18:btab007. doi: 10.1093/bioinformatics/btab007. Epub ahead of print. PMID: 33459763.

BioVenn 1.1.3 / DeepVenn – Comparison and Visualization of Biological lists using Area-proportional Venn diagrams

BioVenn 1.1.3 / DeepVenn

:: DESCRIPTION

BioVenn is an easy-to-use web application to generate area-proportional Venn diagrams from lists of biological identifiers. It supports a wide range of identifiers from the most used biological databases currently available.

DeepVenn – Create Area-Proportional Venn Diagrams Using Deep Learning

::DEVELOPER

Tim Hulsen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser / Linux
  • R / Python

:: DOWNLOAD

BioVenn ,  Python package

:: MORE INFORMATION

Citation:

BMC Genomics. 2008 Oct 16;9:488. doi: 10.1186/1471-2164-9-488.
BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams.
Hulsen T1, de Vlieg J, Alkema W.

jViz.Rna 4.0 – Visual Comparison of RNA Secondary Structure

jViz.Rna 4.0

:: DESCRIPTION

jViz.Rna is a multi-platform visualization tool capable of displaying and comparing RNA secondary structures encoded in a number of file formats. Structures can be shown using six different visualization modes including a numerical analysis mode which includes sensitivity and specificity. Any of the drawings and data produced can be saved in a variety of formats enabling easy usage in publications and presentations.

::DEVELOPER

jViz.Rna Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 jViz.Rna

:: MORE INFORMATION

Citation:

Shabash B, Wiese KC.
jViz.RNA 4.0-Visualizing pseudoknots and RNA editing employing compressed tree graphs.
PLoS One. 2019 May 6;14(5):e0210281. doi: 10.1371/journal.pone.0210281. PMID: 31059508; PMCID: PMC6502502.

Kay C. Wiese and Edward Glen (2006),
jViz.Rna – An Interactive Graphical Tool for Visualizing RNA Secondary Structure Including Pseudoknots
Proceedings of the 19th International Symposium on Computer Based Medical Systems (IEEE/CBMS-2006), June 2006, pp 659-664.

ENNB – Feature Selection and Comparison in Functional Analysis of Metagenomes

ENNB

:: DESCRIPTION

ENNB is a two-stage statistical procedure for feature selection and comparison in functional analysis of metagenomes.In the first stage of the proposed procedure, the informative features are selected using Elastic Net as reducing the dimension of metagenomic data; in the second stage the differentially abundant features are detected using generalized linear models with a Negative Binomial distribution.

::DEVELOPER

Lingling An

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 ENNB

:: MORE INFORMATION

Citation

A two-stage statistical procedure for feature selection and comparison in functional analysis of metagenomes.
Pookhao N, Sohn M, Li Q, Jenkins I, Du R, Jiang H, An L.
Bioinformatics. 2014 Sep 24. pii: btu635.

Rclick – Comparison of RNA 3D Structures

Rclick

:: DESCRIPTION

Rclick is capable of superimposing the RNA 3D structures by using the algorithm of clique matching and 3D least squares fitting.

::DEVELOPER

Rclick team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Rclick: A web server for comparison of RNA 3D structures.
Nguyen MN, Verma C.
Bioinformatics. 2014 Nov 12. pii: btu752.

CONSRANK – Analysis,Comparison and Ranking of Docking Models based on Inter-residue Contacts

CONSRANK

:: DESCRIPTION

CONSRANK (CONSensus-RANKing) is a web service to easily and effectively analyse and rank docking models of protein-protein and protein-nucleic acid complexes, based on the frequency of inter-residue contacts.

::DEVELOPER

MoLNaC: Modeling Lab for Nanostructures and Catalysis 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation:

CONSRANK: a server for the analysis, comparison and ranking of docking models based on inter-residue contacts.
Chermak E, Petta A, Serra L, Vangone A, Scarano V, Cavallo L, Oliva R.
Bioinformatics. 2014 Dec 21. pii: btu837.

d2Meta – Comparison of Metagenomic Samples Using Sequence Signatures

d2Meta

:: DESCRIPTION

d2Meta is intended to implement a program for alignment-free comparison of metagenomic samples of NGS data using  and .

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • C++ Compiler

:: DOWNLOAD

 d2Meta

:: MORE INFORMATION

Citation

BMC Genomics. 2012 Dec 27;13:730. doi: 10.1186/1471-2164-13-730.
Comparison of metagenomic samples using sequence signatures.
Jiang B, Song K, Ren J, Deng M, Sun F, Zhang X.

OrthoVenn2 – Comparison and Annotation of Orthologous Gene Clusters among multiple Species

OrthoVenn2

:: DESCRIPTION

OrthoVenn2 is a web platform for comparison and annotation of orthologous gene clusters among multiple species.

::DEVELOPER

OrthoVenn team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Xu L, Dong Z, Fang L, Luo Y, Wei Z, Guo H, Zhang G, Gu YQ, Coleman-Derr D, Xia Q, Wang Y.
OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species.
Nucleic Acids Res. 2019 Jul 2;47(W1):W52-W58. doi: 10.1093/nar/gkz333. PMID: 31053848; PMCID: PMC6602458.

OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species.
Wang Y, Coleman-Derr D, Chen G, Gu YQ.
Nucleic Acids Res. 2015 May 11. pii: gkv487.