ArticleNucleic acids research2016
SimpleSynteny: a web-based tool for visualization of microsynteny across multiple species.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers.
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Who cites it
78 citing papers in PubMed.
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- The Complete Chloroplast Genome of Tree Fern Cyathea delgadii and Its Comparison to Other Cyatheales.Biochemical genetics · 2026Article
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- Arsenotrophic Achromobacter aegrifaciens strains isolated from arsenic contaminated tubewell water and soil sources shared similar genomic potentials.BMC microbiology · 2024Article
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- Insights into the genomic and functional divergence of NAT gene family to serve microbial secondary metabolism.Scientific reports · 2024Article
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- Analysis of Ice-Binding Protein Evolution.Methods in molecular biology (Clifton, N.J.) · 2024Article
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- DiGAlign: Versatile and Interactive Visualization of Sequence Alignment for Comparative Genomics.Microbes and environments · 2024Article
- Identification of Virulence Factors in EntomopathogenicMicroorganisms · 2023Article
18 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Defining syntenic relationships among orthologous gene clusters is a frequent undertaking of biologists studying organismal evolution through comparative genomic approaches. With the increasing availability of genome data made possible through next-generation sequencing technology, there is a growing need for user-friendly tools capable of assessing synteny. Here we present SimpleSynteny, a new 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. 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. SimpleSynteny is freely available at: http://www.SimpleSynteny.com.
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