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Displays large volumes of genomic rearrangement data. Circos is a visualization tool that applies a circular ideogram layout to display relationships between genomic intervals. The software provides a scalable means to illustrate relationships between genomic positions and is designed to allow flexible and easy rearrangement of elements in the image. It also contains several tools to help analyze, filter, and format data.
A comparative genomic visualization tool that combines three complementary displays: (i) a table for thoroughly browsing amongst homologues, (ii) a comparator of orthologue functional annotations and (iii) a genomic organization view designed to improve the legibility of rearrangements and distinctive loci. The latter display combines symbolic and proportional graphical paradigms. Synchronized navigation across multiple species and interoperability between the views are core features of Insyght. A gene filter mechanism is provided that helps the user to build a biologically relevant gene set according to multiple criteria such as presence/absence of homologues and/or various annotations.
Provides a feature-rich set of comparative genomics tools for inspection of multiple genome structures, mining of orthologous gene families and identification of potential vaccine candidates. The Sybil suite of feature-rich web tools allows users to search and visualize several genomes based on clusters of orthologous genes. The views in Sybil are interactive allowing users to click on each drawn feature to retrieve more detailed information. Navigation between views is supported and provides Sybil with the unique ability to explore from the whole genome level to the protein and nucleotide multiple sequence alignment level without leaving the application. Export of tab-delimited tables, sequence data, and SVG and PDF publication-quality figures is possible from many of the views.
A web-based platform capable of directly interrogating collinearity of local genomic neighbors across multiple species in a targeted manner. SimpleSynteny provides a pipeline for evaluating the synteny of a preselected set of gene targets across multiple organismal genomes. The standard pipeline for SimpleSynteny consists of three primary steps: (1) data input, (2) contig editing and (3) customization of graphical output. An emphasis has been placed on ease-of-use, and users are only required to submit FASTA files for their genomes and genes of interest. SimpleSynteny then guides the user through an iterative process of exploring and customizing genomes individually before combining them into a final high-resolution figure. Because the process is iterative, it allows the user to customize the organization of multiple contigs and incorporate knowledge from additional sources, rather than forcing complete dependence on the computational predictions. Additional tools are provided to help the user identify which contigs in a genome assembly contain gene targets and to optimize analyses of circular genomes.
Allows to compare synteny between three genomes in a 3D environment. SynMap3D is a web-based whole-genome synteny browser that both identifies and visualizes regions of synteny. Results are displayed as a three dimensional dotplot (scatter plot), with each axis representing a linearized version of the genome. The software also includes the option to enable virtual reality (VR) mode, allowing researchers with a VR headset to interact with their data in an immersive, responsive environment.
Synima / Synteny Imager
Allows visualization of chains of predicted orthologs between two or more genomes. Synima includes, in addition to visualizing synteny, a pipeline for predicting and generating chains of orthologs between any number of genomes. The software has been developed and tested on a range of datasets, including up to 12 genomes of 17.2–18.3 million bases long each. It can be useful for researchers interested in synteny between two or more annotated genome assemblies, and highlighting genes of interest among them.
Allows multiple synteny determination and visualization between user’s genomic data and/or published plant genome data. MultiSyn allows users to set regions of interest of species against the 18 plants provided in the webtool by choosing a species, chromosome, and input locus information at the start and end positions. It aims to aid evolutionary analysis by displaying multiple synteny. The tool provides a convenient means for biologists to analyze their sequence of interest.
A standalone web-based tool that provides an in-depth view of gene structure across gene families, with various options to render and filter visualisations. Aequatus relies on pre-calculated alignment and gene feature information held in an Ensembl database, typically generated through the Ensembl Compara workflow. We also offer Aequatus.js, a reusable JavaScript module that fulfils the visualisation aspects of Aequatus. As a part of the Aequatus project, we have developed Aequatus.js, an open-source JavaScript library. We have extracted the visualisation modules from the standalone Aequatus browser in order to make the tool more accessible and reusable.
Allows visual comparison of genome data. SynView is a light-weight, interactive and customizable comparative genomic visualization tool based on the GBrowse framework. The software can read mapping data and allow user to compare multiple genomes at several scales. It was developed for use in the CryptoDB project and has since been adopted by the PlasmoDB project to compare several genomes that are more divergent than Cryptosporidium. SynView can be integrated with other projects.
GSV / Genome Synteny Viewer
An option for biologists to analyze genome synteny by uploading their own data set to a web-based comparative genome browser. Allows users to upload two data files for synteny visualization, the mandatory synteny file for specifying genomic positions of conserved regions and the optional genome annotation file. GSV presents two selected genomes in a single integrated view while still retaining the browsing flexibility necessary for exploring individual genomes. Users can browse and filter for genomic regions of interest, change the color or shape of each annotation track as well as re-order, hide or show the tracks dynamically. Additional features include downloadable images, immediate email notification and tracking of usage history. The entire GSV package is also light-weighted which enables easy local installation.
mGSV / multi-Genome Synteny Viewer
A web-based synteny visualization tool that enhances the original functionalities of GSV by allowing biologists to upload their own datasets and visualize the synteny among multiple genomes simultaneously in a single integrated view. Users can navigate through all the selected genomes in either pairwise or multiple viewing mode to examine conserved genomic regions as well as the accompanying genome annotations. Besides serving users who manually interact with the web server, mGSV also provides Web Services for machine-to-machine communication to accept data sent by other remote resources. The novel design and the implementation of mGSV provide the research community with an important alternative to currently available tools. Multiple genomes can be presented in a single integrated view with an enhanced user interface.
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