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.
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.
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.
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.
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.