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SynTView

SynTView is a recently published interactive multi-view genome browser for next-generation comparative microorganism genomics. The software is characterised by the presentation of syntenic organisations of microbial genomes and the visualisation of polymorphism data obtained from next generation sequencing. SynTView is built as a generic genome browser including sub-maps that hold information about genomic objects. After selecting genomes of interest, the users can explore them visually by genomic location, or directly go to specific genes by name. Several genomic maps can be stacked on top of each other. The creation of a SynTView website is very helpful in the analysis of a large number of strains, bringing together phylogeny, polymorphisms, larger variants such as indels, coverage, as well as functional annotations and strains meta-data. SynTView is designed to visualise information about polymorphism across a large number of bacterial strains. The SNP maps allow the user to navigate through polymorphism data sets. SynTView has been integrated to the Listeriomics web site, a platform for visualizing and analysing every heterogeneous Listeria "omics" dataset published to date.

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Institution: Institut Pasteur, Paris, France

PlantGenIE

The Plant Genome Integrative Explorer is a collection of interoperable web resources for searching, visualizing and analyzing genomics and transcriptomics data for different plant species. Currently it includes dedicated web portals for enabling in-depth exploration of poplar, Norway spruce, and Arabidopsis. The PlantGenIE platform uses Chado databases and is based on the GenIE CMS (Content Management System). Standard features of a model organism database are provided, including genome browsers, gene list annotation, Blast homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. PlantGenIE includes RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the ComPlEx resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated.

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Institution: Umeå University

BioJS

BioJS is a library of over hundred JavaScript components enabling you to visualize and process data using current web technologies.

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Institution: BioJS

Integrated Genome Browser

The Integrated Genome Browser (IGB, pronounced Ig-Bee) is a fast, flexible, and free desktop genome browser. First developed at Affymetrix in 2001 to support visual analytics of genome tiling arrays, IGB provides an advanced, highly customizable environment for exploring and analyzing large-scale genomic data sets.

Using IGB, you can:

  • View your RNA-Seq, ChIP-chip or ChIP-seq data alongside genome annotations and sequence.
  • Investigate alternative splicing, regulation of gene expression, epigenetic modifications of DNA, and other genome-scale questions.
  • View results from aligning short-read sequences onto a target genome, identify SNPs, and check alignment quality.
  • Copy and paste genomic sequences for further analysis into other tools, such as primer design and promoter analysis tools.
  • Create high-quality images for publication in a variety of formats.

 

IGB features

IGB lets you view results from your own experiments or computational analyses alongside public domain gene annotations, sequences, and genomic data sets, thus making it easier for you to determine how your experiments agree or disagree with current thinking and models of genomic structure.

Some features IGB offers include:

  • Animated zooming. Most genome browsers implement "jump zooming" only, in which you click a zoom button (or other type of control) and then wait for the display to re-draw. In IGB, zooming is animated, allowing you to easily and quickly adjust the zoom level as needed without losing track of your location.
  • Simple Data Sharing System - QuickLoad. IGB implements a very simple, easy-to-use system for sharing data called QuickLoad. You can use the QuickLoad system to set up a Web site you can use to share your data with colleagues, reviewers, and the public.
  • Draggable graphs. You can display genome graphs data (e.g., "bar" and "wiggle" files) alongside and even on top of reference genome annotations, thus making it easier to see how your experimental results match up to the published reference genome annotations. You can reset your graphs to "floating" and click-drag them over annotations to compare your results with annotations and others' experiments.
  • Edge-matching across tracks. When you click an item in the display, the edges of other items in the same or different tracks with identical boundaries light up, highlighting interesting similarities or differences across gene models, sequence reads, or other features.
  • Integration with local and remote external data sources. IGB can load data from a variety of sources, including Distributed Annotation Servers, QuickLoad servers, ordinary Web sites, and local files.
  • Intron-trimming sliced view. In many species, introns are huge when compared to the exonic (coding) regions of genes. IGB provides a Sliced View tab that trims uninformative regions from introns.
  • Web-controls. IGB can be controlled from a web browser or any other program capable of sending HTTP requests. Via IGB links, you can create Web pages that direct IGB to scroll to a specific region and load data sets from local files or servers.
  • Scripting. IGB understands a simple command language that allows users to write simple scripts directing IGB to show a genome, zoom and scroll to specific regions, and other functions.
  • Open source. All development on IGB proceeds via a 100% open source model. The license allows developers to incorporate IGB (and its components) into new applications.
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Institution: UNC @ Charlotte

Sequence Bundles

Sequence Bundles is a new tool for visualising and exploring sequence motifs in multiple sequence alignment (MSA) data.

It enables the discovery of data features that would otherwise remain hidden.

In Sequence Bundles, MSA sequences are visualised as continuous strings of data, which helps in preserving and exposing important residue correlations.

Use Sequence Bundles web tool to easily look at your own MSA data in a completely new way.

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Institution: Science Practice

Sequence Bundles were designed by Science Practice in collaboration with Goldman group at the EMBL-EBI. For more details visit Sequence Bundles project homepage and read our article: BMC Proceedings 2014, 8(Suppl 2):S8

Sequence logo viewer

Web-based sequence logo viewer

Developed for the BioVis 2012 Redesign Contest, this tool provides a sequence logo using glyph-based approaches to aid interpretation.

This can be deployed using an easy to use JavaScript library that uses Raphael.js to render visualization of one or more sequence logos.

It supports DNA, RNA, and amino acid sequences.


Cite this work

E. Maguire, P. Rocca-Serra, S.-A. Sansone, and M. Chen, Redesigning the sequence logo with glyph-based approaches to aid interpretation, In Proceedings of EuroVis 2014, Short Paper (2014)

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Aequatus

We present the Aequatus, a web-based tool with novel rendering approaches to visualise homologous, orthologous and paralogous gene structures among differing species or subtypes of a common species. The Aequatus utilises web technologies to provide a fast and intuitive browsing experience over complex comparative data. The Aequatus processes and visualises data directly from the Ensembl Compara and Ensembl Core schema databases by using precalculated genomic alignments from Ensembl Compara and relating them to Ensembl Core to gather genomic feature information, visualising phylogenetic and structural relationships among them via CIGAR strings. Whilst applicable to species with high-quality gold-standard reference genomes such as human or mouse, the Aequatus was designed with large fragmented genome references in mind,  e.g. polyploid plants. The ultimate goal of the Aequatus is to provide a unique and informative way to render and explore complex relationships between genes from various species.

Source Code: https://github.com/TGAC/Aequatus

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Institution: Earlham Institute

TGAC Browser

We present the TGAC Browser with novel rendering, annotation and analysis capabilities designed to overcome the shortcomings in available approaches. TGAC Browser, being a web-based client, utilises JavaScript libraries to provide a fast and intuitive genome browsing experience. We focus on harnessing Internet architectures as well as localised HPC hardware, concentrating on improved, more productive interfaces and analytical capabilities.

  • User-friendly: Live data searching, track modification, and drag and drop selection; actions that are seamlessly powered by modern web browser
  • Responsiveness: Client-side rendering and caching, based on JSON fragments generated by server logic, helps decrease the server load and improves user experience
    • TGAC Browser visualises genomic data in different ways, based on the type and amount of data, which is more informative to the user and memory efficien
  • Analysis Integration: The ability to carry out heavyweight analysis tasks, using tools such as BLAST, via a dedicated extensible daemon
  • Annotation: Users can edit annotations which can be persisted on the server, reloaded, and shared at a later date
  • Off-the-shelf Installation: The only prerequisites are a web application container, such as Jetty or Tomcat, and a standard Ensembl database to host sequence features
  • Extensible: Adaptable modular design to enable interfacing with other databases, e.g. GMOD
  • Data format: TGAC Browser processes and visualises data directly from the Ensembl core schema as well as next-generation sequencing (NGS) data output, i.e. BAM/SAM, BigWig/wig, GFF, and VCF.
  • Manual Annotation: Live editing of Genomics annotations within TGAC Browser, saved with versions and can be reverted, exported in Genomics data format for curator to edit datasets (Under development).

Email: Anil.Thanki@earlham.ac.uk

Source Code: https://github.com/tgac/tgacbrowser

 

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Institution: Earlham Institute

Pipit

Pipit is a gene-centric interactive visualization tool designed to study structural genomic variations. Through focusing on individual genes as the functional unit, researchers are able to study and generate hypotheses on the biological impact of different structural variations, for instance, the deletion of dosage-sensitive genes or the formation of fusion genes. Pipit is a cross-platform Java application that visualizes structural variation data from Genome Variation Format files.

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Institution: KU Leuven

ArkMAP

ArkMAP is a desktop application to draw and align genetic and genomic maps, retrieved from remote data sources or loaded as local files. Maps can be retrieved from our public map database ArkDB or from any Ensembl data source (i.e. Ensembl and Ensembl Genomes). By using the JEnsembl API, maps can be drawn for any release version of any of the thousands of species present in Ensembl data sources, allowing not only inter-specific comparisons, but also comparisons between different versions/revisions of assembled genomes. Maps can be aligned by relating identical or synonymous markers across maps, or through the gene homology/orthology relationship data stored in the Ensembl Compara databases, allowing ready visualization of regions of conserved synteny between species. The map drawing canvas is highly configurable, supports interactive exploration of maps, markers and relationships and allows export of publication quality graphics.

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Institution: University of Edinburgh

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