Tag: Browser

GEB – Genome Environment Browser

GEB

:: DESCRIPTION

GEB is a Java application developed to provide a dynamic graphical interface to visualise the distribution of genome features and chromosome-wide experimental data in high resolution.

::DEVELOPER

the Bioinformatics Support Service, Centre for Bioinformatics, Imperial College London, UK and the MRC Clinical Sciences Centre, London, UK

:: SCREENSHOTS

GEB

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Java
  • MySQL 

:: DOWNLOAD

 GEB

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2008 Nov 27;9:501. doi: 10.1186/1471-2105-9-501.
Genome Environment Browser (GEB): a dynamic browser for visualising high-throughput experimental data in the context of genome features.
Huntley D, Tang YA, Nesterova TB, Butcher S, Brockdorff N.

ECR Browser – Interactive Browser of Genome Conservation and Evolution

ECR Browser

:: DESCRIPTION

The ECR Browser is a dynamic graphical interface that allows users to visualize and analyze Evolutionary Conserved Regions (ECRs) in genomes of sequenced species.

::DEVELOPER

Ivan Ovcharenko Research Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes.
Ovcharenko I, Nobrega MA, Loots GG, Stubbs L.
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W280-6.

Pathway Projector – Zoomable Pathway Browser using KEGG Atlas

Pathway Projector

:: DESCRIPTION

The Pathway Projector was implemented according to the aforementioned requirements, including the availability of a large-scale comprehensive pathway map, pathways from a wide variety of organisms, and searching and mapping capabilities.

::DEVELOPER

PathwayProjector team

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser 
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.
Kono N, Arakawa K, Ogawa R, Kido N, Oshita K, Ikegami K, Tamaki S, Tomita M.
PLoS One. 2009 Nov 11;4(11):e7710. doi: 10.1371/journal.pone.0007710.

seeQTL – A Searchable Human eQTL Browser and database

seeQTL

:: DESCRIPTION

seeQTL is a comprehensive and versatile eQTL database, including various eQTL studies and a meta-analysis of HapMap eQTL information. The database presents eQTL association results in a convenient browser, using both segmented local-association plots and genome-wide Manhattan plots.

::DEVELOPER

Department of Biostatistics, Computer Sciences and Genetics, University of North Carolina at Chapel Hill

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web  Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

K. Xia, A.A. Shabalin, S. Huang, V. Madar, Y.H. Zhou, W. Wang, F. Zou, W. Sun, P.F. Sullivan, and F.A. Wright
seeQTL: A searchable database for human eQTLs
Bioinformatics (2012) 28(3): 451-452

SHIPREC – Salmonella/Host Protein-Protein Interaction Predictions Browser

SHIPREC

:: DESCRIPTION

SHIPREC is a Salmonella/Host Protein-Protein Interaction Predictions Browser.

::DEVELOPER

Structural BioInformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No

:: MORE INFORMATION

Citation

Chem Biodivers. 2012 May;9(5):991-1018. doi: 10.1002/cbdv.201100392.
Prediction and comparison of Salmonella-human and Salmonella-Arabidopsis interactomes.
Schleker S, Garcia-Garcia J, Klein-Seetharaman J, Oliva B.

DiProGB 20100209 – The Dinucleotide Properties Genome Browser

DiProGB 20100209

:: DESCRIPTION

DiProGB is a genome browser that encodes the genome sequence by physico-chemical dinucleotide properties such as stacking energy, melting temperature or twist angle. Analyses can be performed for the + and –, as well as for the double strand.

::DEVELOPER

Dr. Maik Friedel

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 DiProGB

:: MORE INFORMATION

Citation

M Friedel, S Nikolajewa, J Suehnel, T Wilhelm.
DiProGB: The Dinucleotide Properties Genome Browser
Bioinformatics 25 (2009) 2603-2604.

 

NGV 0.1 – Browser for Efficient Display of Large HTS Data Sets

NGV 0.1

:: DESCRIPTION

NGV (Next Generation Viewer) is a Preprocessor and Browser for efficient display of large HTS Data Sets. In a preprocessing step, NGV takes a genomic sequence and a file containing mapped reads as input and creates several indices. This preprocessing step is easily extendable by a plug-in mechanism. Preprocessed data sets can then be loaded and visualized efficiently: NGV provides several information visualizations (coverage histogram, coverage overviews, detail view). It makes use of interval tree-based indices to efficiently visualize large HTS data sets and enable users to search for regions with a defined minimum coverage as well as for mismatches between consensus and reference sequence.

::DEVELOPER

 the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

  NGV

:: MORE INFORMATION

SPICE 0.9 – Protein Sequences, Structures & Annotations Browser

SPICE 0.9

:: DESCRIPTION

SPICE is a browser for protein sequences, structures and their annotations. It can display annotations for PDB, UniProt and Ensembl Peptides. All data is retrieved from different sites on the Internet, that make their annotations available using the DAS protocol. It is possible to add new annotations to SPICE, and to compare them with the already available information.

::DEVELOPER

Andreas Prlic, Thomas Down, Tim Hubbard.

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

SPICE

:: MORE INFORMATION

Citation:

Adding some SPICE to DAS
Bioinformatics Volume 21, suppl_2 Pp. ii40-ii41
Andreas Prlic, Thomas A. Down and Tim J. P. Hubbard

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