Synteny Visualization Research Articles

An online database foreinkorn wheat to aid ingene discovery andfunctional genomics studies.

Diploid A-genome wheat (einkorn wheat) presents a nutrition-rich option as an ancient grain crop and a resource for the improvement of bread wheat against abiotic and biotic stresses. Realizing the importance of this wheat species, reference-level assemblies of two einkorn wheat accessions were generated (wild and domesticated). This work reports an einkorn genome database that provides an interface to the cereals research community to perform comparative genomics, applied genetics and breeding research. It features queries for annotated genes, the use of a recent genome browser release, and the ability to search for sequence alignments using a modern BLAST interface. Other features include a comparison of reference einkorn assemblies with other wheat cultivars through genomic synteny visualization and an alignment visualization tool for BLAST results. Altogether, this resource will help wheat research and breeding. Database URL https://wheat.pw.usda.gov/GG3/pangenome.

Synima: a Synteny imaging tool for annotated genome assemblies

BackgroundOrtholog prediction and synteny visualization across whole genomes are valuable methods for detecting and representing a range of evolutionary processes such as genome expansion, chromosomal rearrangement, and chromosomal translocation. Few standalone methods are currently available to visualize synteny across any number of annotated genomes.ResultsHere, I present a Synteny Imaging tool (Synima) written in Perl, which uses the graphical features of R. Synima takes orthologues computed from reciprocal best BLAST hits or OrthoMCL, and DAGchainer, and outputs an overview of genome-wide synteny in PDF. Each of these programs are included with the Synima package, and a pipeline for their use. Synima has a range of graphical parameters including size, colours, order, and labels, which are specified in a config file generated by the first run of Synima – and can be subsequently edited. Synima runs quickly on a command line to generate informative and publication quality figures. Synima is open source and freely available from https://github.com/rhysf/Synima under the MIT License.ConclusionsSynima should be a valuable tool for visualizing synteny between two or more annotated genome assemblies.

SynMap2 and SynMap3D: web-based whole-genome synteny browsers

Current synteny visualization tools either focus on small regions of sequence and do not illustrate genome-wide trends, or are complicated to use and create visualizations that are difficult to interpret. To address this challenge, The Comparative Genomics Platform (CoGe) has developed two web-based tools to visualize synteny across whole genomes. SynMap2 and SynMap3D allow researchers to explore whole genome synteny patterns (across two or three genomes, respectively) in responsive, web-based visualization and virtual reality environments. Both tools have access to the extensive CoGe genome database (containing over 30 000 genomes) as well as the option for users to upload their own data. By leveraging modern web technologies there is no installation required, making the tools widely accessible and easy to use. Both tools are open source (MIT license) and freely available for use online through CoGe ( https://genomevolution.org ). SynMap2 and SynMap3D can be accessed at http://genomevolution.org/coge/SynMap.pl and http://genomevolution.org/coge/SynMap3D.pl , respectively. Source code is available: https://github.com/LyonsLab/coge . ericlyons@email.arizona.edu. Supplementary data are available at Bioinformatics online.

Synteny Explorer: An Interactive Visualization Application for Teaching Genome Evolution.

Rapid advances in biology demand new tools for more active research dissemination and engaged teaching. This paper presents Synteny Explorer, an interactive visualization application designed to let college students explore genome evolution of mammalian species. The tool visualizes synteny blocks: segments of homologous DNA shared between various extant species that can be traced back or reconstructed in extinct, ancestral species. We take a karyogram-based approach to create an interactive synteny visualization, leading to a more appealing and engaging design for undergraduate-level genome evolution education. For validation, we conduct three user studies: two focused studies on color and animation design choices and a larger study that performs overall system usability testing while comparing our karyogram-based designs with two more common genome mapping representations in an educational context. While existing views communicate the same information, study participants found the interactive, karyogram-based views much easier and likable to use. We additionally discuss feedback from biology and genomics faculty, who judge Synteny Explorer's fitness for use in classrooms.

A web-based multi-genome synteny viewer for customized data.

BackgroundWeb-based synteny visualization tools are important for sharing data and revealing patterns of complicated genome conservation and rearrangements. Such tools should allow biologists to upload genomic data for their own analysis. This requirement is critical because individual biologists are generating large amounts of genomic sequences that quickly overwhelm any centralized web resources to collect and display all those data. Recently, we published a web-based synteny viewer, GSV, which was designed to satisfy the above requirement. However, GSV can only compare two genomes at a given time. Extending the functionality of GSV to visualize multiple genomes is important to meet the increasing demand of the research community.ResultsWe have developed a multi-Genome Synteny Viewer (mGSV). Similar to GSV, mGSV is a web-based tool that allows users to upload their own genomic data files for visualization. Multiple genomes can be presented in a single integrated view with an enhanced user interface. 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 entire mGSV package can also be downloaded for easy local installation.ConclusionsmGSV significantly enhances the original functionalities of GSV. A web server hosting mGSV is provided at http://cas-bioinfo.cas.unt.edu/mgsv.

GSV: a web-based genome synteny viewer for customized data.

BackgroundThe analysis of genome synteny is a common practice in comparative genomics. With the advent of DNA sequencing technologies, individual biologists can rapidly produce their genomic sequences of interest. Although web-based synteny visualization tools are convenient for biologists to use, none of the existing ones allow biologists to upload their own data for analysis.ResultsWe have developed the web-based Genome Synteny Viewer (GSV) that 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.ConclusionsGSV provides a unique option for biologists to analyze genome synteny by uploading their own data set to a web-based comparative genome browser. A web server hosting GSV is provided at http://cas-bioinfo.cas.unt.edu/gsv, and the software is also freely available for local installations.

Rapid pair-wise synteny analysis of large bacterial genomes using web-based GeneOrder4.0

BackgroundThe growing whole genome sequence databases necessitate the development of user-friendly software tools to mine these data. Web-based tools are particularly useful to wet-bench biologists as they enable platform-independent analysis of sequence data, without having to perform complex programming tasks and software compiling.FindingsGeneOrder4.0 is a web-based "on-the-fly" synteny and gene order analysis tool for comparative bacterial genomics (ca. 8 Mb). It enables the visualization of synteny by plotting protein similarity scores between two genomes and it also provides visual annotation of "hypothetical" proteins from older archived genomes based on more recent annotations.ConclusionsThe web-based software tool GeneOrder4.0 is a user-friendly application that has been updated to allow the rapid analysis of synteny and gene order in large bacterial genomes. It is developed with the wet-bench researcher in mind.

OrthoClusterDB: an online platform for synteny blocks

BackgroundThe recent availability of an expanding collection of genome sequences driven by technological advances has facilitated comparative genomics and in particular the identification of synteny among multiple genomes. However, the development of effective and easy-to-use methods for identifying such conserved gene clusters among multiple genomes–synteny blocks–as well as databases, which host synteny blocks from various groups of species (especially eukaryotes) and also allow users to run synteny-identification programs, lags behind.DescriptionsOrthoClusterDB is a new online platform for the identification and visualization of synteny blocks. OrthoClusterDB consists of two key web pages: Run OrthoCluster and View Synteny. The Run OrthoCluster page serves as web front-end to OrthoCluster, a recently developed program for synteny block detection. Run OrthoCluster offers full control over the functionalities of OrthoCluster, such as specifying synteny block size, considering order and strandedness of genes within synteny blocks, including or excluding nested synteny blocks, handling one-to-many orthologous relationships, and comparing multiple genomes. In contrast, the View Synteny page gives access to perfect and imperfect synteny blocks precomputed for a large number of genomes, without the need for users to retrieve and format input data. Additionally, genes are cross-linked with public databases for effective browsing. For both Run OrthoCluster and View Synteny, identified synteny blocks can be browsed at the whole genome, chromosome, and individual gene level. OrthoClusterDB is freely accessible.ConclusionWe have developed an online system for the identification and visualization of synteny blocks among multiple genomes. The system is freely available at .