Webina 1.0.0 – A JavaScript/WebAssembly library that runs Vina in a browser

Webina 1.0.0

:: DESCRIPTION

Webina is a JavaScript/WebAssembly library that runs AutoDock Vina entirely in a web browser. The docking calculations take place on the user’s own computer rather than a remote server.

::DEVELOPER

Durrant Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

Webina

:: MORE INFORMATION

Citation

Webina: An Open-Source Library and Web App that Runs AutoDock Vina Entirely in the Web Browser
Yuri Kochnev, Erich Hellemann, Kevin C. Cassidy, View ORCID ProfileJacob D. Durrant
doi: https://doi.org/10.1101/2019.12.18.881789

ProteinVR 1.0.3 – Browser-based, virtual-reality visualization of Molecular Structures

ProteinVR 1.0.3

:: DESCRIPTION

ProteinVR is a web-based application that allows users to view protein/ligand structures in virtual reality (VR) from their mobile, desktop, or VR-headset-based web browsers. Molecular structures are displayed within 3D environments that give useful biological context and allow users to situate themselves in 3D space.

::DEVELOPER

Durrant Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

ProteinVR

:: MORE INFORMATION

 

MEME-LaB – Motif analysis in Clusters

MEME-LaB

:: DESCRIPTION

MEME-LaB (MEME Launcher and Browser) provides an interface to run MEME on a range of gene clusters and browse the resulting motifs

::DEVELOPER

Warwick Systems Biology Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 1;29(13):1696-7. doi: 10.1093/bioinformatics/btt248. Epub 2013 May 16.
MEME-LaB: motif analysis in clusters.
Brown P, Baxter L, Hickman R, Beynon J, Moore JD, Ott S.

AGB – Ancestral Genome Browser

AGB

:: DESCRIPTION

AGB is a website which provides the ancestral organisms genomic information. It builds on genetic resources of existent living things.

::DEVELOPER

Bioinformatics Laboratory, Konkuk University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Lee D, Lee J, Hong WY, Jang E, and Kim J,
AGB (Ancestral Genome Browser): A Web Interface for Browsing Reconstructed Ancestral Genomes,
Journal of KIISE, 42(12):1584-1589, 2015

Aequatus – Open-source Homology Browser

Aequatus

:: DESCRIPTION

Aequatus is an open-source web-based tool to visualise homologous gene structures among differing species or subtypes of a common species.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser/ Linux

:: DOWNLOAD

Aequatus

:: MORE INFORMATION

Citation

Aequatus: an open-source homology browser.
Thanki AS, Soranzo N, Herrero J, Haerty W, Davey RP.
Gigascience. 2018 Nov 1;7(11). doi: 10.1093/gigascience/giy128.

RPAN 0.91 – Rice Pan-genome Browser for 3K rice genomes

RPAN 0.91

:: DESCRIPTION

RPAN is a genome browser to search and visualize the rice pan-genome derived from 3K RGP. RPAN contains a database of the basic information of 3010 rice accessions, including genomic sequences, gene annotations, PAV information and gene expression data of the rice pan-genome. At least 12 000 novel genes absent in the reference genome were included. RPAN also provides multiple search and visualization functions. RPAN can be a rich resource for rice biology and rice breeding.

::DEVELOPER

Dr. Chaochun Wei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser / Linux with apache server.

:: DOWNLOAD

RPAN

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2017 Jan 25;45(2):597-605. doi: 10.1093/nar/gkw958. Epub 2016 Dec 10.
RPAN: rice pan-genome browser for ~3000 rice genomes.
Sun C et al.

MochiView 1.46 – Genomic Sequences Browser

MochiView 1.46

:: DESCRIPTION

MochiView is Java software that integrates browsing of genomic sequences, features, and data with DNA motif visualization and analysis

::DEVELOPER

the Johnson Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • Java

:: DOWNLOAD

 MochiView

:: MORE INFORMATION

Citation

Oliver R Homann and Alexander D Johnson
MochiView: versatile software for genome browsing and DNA motif analysis
BMC Biology 2010, 8:49

Artemis v18.0.3 – Genome Browser and Annotation Tool

Artemis v18.0.3

:: DESCRIPTION

Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation.

::DEVELOPER

the Sanger Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • Java

:: DOWNLOAD

Artemis

:: MORE INFORMATION

Citation

Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA and Barrell B
Artemis: sequence visualization and annotation.
Bioinformatics (Oxford, England) 2000;16;10;944-5

Wasabi 20151112 – Powerful Multiple Sequence Alignment Browser

Wasabi 20151112

:: DESCRIPTION

Wasabi is a tool for visualisation and manipulation of rich MSAs and a graphical interface to command-line programs.

::DEVELOPER

Löytynoja Lab

:: SCREENSHOTS

Wasabi

:: REQUIREMENTS

  • Linux/ Windows /MacOsX
  • Java

:: DOWNLOAD

 Wasabi

:: MORE INFORMATION

Citation

Wasabi: An Integrated Platform for Evolutionary Sequence Analysis and Data Visualization.
Veidenberg A, Medlar A, Löytynoja A.
Mol Biol Evol. 2016 Apr;33(4):1126-30. doi: 10.1093/molbev/msv333.

GenoViewer 0.9.0 – Viewer/Browser for the Sam/Bam format

GenoViewer 0.9.0

:: DESCRIPTION

GenoViewer is a comprehensive and open source viewer/browser for the sam/bam format commonly used in the assembly tasks of Next Generation Sequencing data.

::DEVELOPER

Astrid Research, Inc.

:: SCREENSHOTS

GenoViewer

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java 

:: DOWNLOAD

 GenoViewer

:: MORE INFORMATION

Citation

Bioinformation. 2012;8(2):107-9. Epub 2012 Jan 20.
Geno viewer, a SAM/BAM viewer tool.
Laczik M, Tukacs E, Uzonyi B, Domokos B, Doma Z, Kiss M, Horváth A, Batta Z, Maros-Szabó Z, Török Z.