Information on multiple synteny between plants and/or within a plant is key information to understand genome evolution. In addition, visualization of multiple synteny is helpful in interpreting evolution.
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.
Allows users to visualize and analyze evolutionary conserved regions (ECRs) in genomes of sequenced species. Since its initial implementation, when only the genomes of human and mouse were available, the ECR browser has been constantly expanding to include newly sequenced genomes, and now covers 13 species. ECR Browser provides the starting point for discovery of novel genes, identification of distant gene regulatory elements and prediction of transcription factor binding sites. The genome alignment portal of the ECR Browser also permits fast and automated alignments of any user-submitted sequence to the genome of choice. The interconnection of the ECR Browser with other DNA sequence analysis tools creates a unique portal for studying and exploring vertebrate genomes.
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.
Simplifies studies on comparative genomics. Synteny Portal is an online application offering easy construction of synteny blocks, intuitive graphical representation with a high-quality image format and easy-to-use querying and browsing functionalities. It enables a user with a lack of computational skills to perform comparative genomic analyses and to download the details of these analyses.
Provides a platform for exposing and visualizing genes in either ancestral and modern chromosomes. Plant Synteny Viewer aims to provide a quick method for determining useful markers or candidate genes. The application allows users to browse among genomes by using a gene name, a modern chromosome nomenclature, or ancestral protochromosome references as well as configurate various displaying parameters.
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.
Provides automated and guided generation of circular visualization of large scale genomics and transcriptomics data. CGDV provides prepackaged karyotype files for various model organisms and generates config file based upon the genomics and transcriptomics data provided by the user. It can be applied to micro-organism such as bacteria and fungi genome, and to large organisms such as human and mouse genome.
Allows comparative analysis of microbial genome information. SynTView is a web-based and desktop-capable Flash software, built as a generic genome browser including sub-maps that hold information about genomic objects. The software can facilitate the investigation of large data sets at the chromosome scale. It is suitable for the exploration of data obtained in next-generation sequencing (NGS)-based population genomic studies.
Allows visualization of conservation of gene adjacency in many prokaryotic genomes. SynteView displays synteny comparison between a reference genome (choosen by the user) and a set of genomes choosen among a total of 600 prokaryotic genomes stored in SynteBase, a dedicated relational database. This application was developed as a web service and provides a local access mode.
Allows users to align and draw genetic and genomic maps. ArkMAP is developed as a tool for general biologists rather than for expert bioinformaticians. It provides the integration of personal mapping data of any type (i.e. sequence, linkage, radiation hybrid, cytogenetic etc.). This tool provides access to ArkDB database of genetic and cytogenetic maps.
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.
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.
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.