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.

PyBamView 1.0.7 – Browser-based application for Visualizing Complex Bam Alignments

PyBamView 1.0.7

:: DESCRIPTION

PyBamView is a python-based application that allows you to view BAM sequence alignments through your web browser.

::DEVELOPER

Melissa Gymrek

:: SCREENSHOTS

pybamview

:: REQUIREMENTS

:: DOWNLOAD

  PyBamView

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Aug 21. pii: btu565. [Epub ahead of print]
PyBamView: a browser based application for viewing short read alignments.
Gymrek M.

Insyght – Conserved Synteny Homolog Browser

Insyght

:: DESCRIPTION

Insyght is a browser that helps navigate among abundant homologies, syntenies and genes annotations.

::DEVELOPER

Insyght team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Synchronized navigation and comparative analyses across Ensembl complete bacterial genomes with INSYGHT.
Lacroix T, Thérond S, Rugeri M, Nicolas P, Gendrault A, Loux V, Gibrat JF.
Bioinformatics. 2015 Nov 24. pii: btv689.