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SimpleSynteny: a web-based tool for visualization of microsynteny across multiple species
Daniel Veltri1, Martha Malapi Wight2, Jo Anne Crouch3
1Systematic Mycology and Microbiology Laboratory, U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), 10300 Baltimore Avenue, Building 10A, Beltsville, MD 20705, USA Oak Ridge Institute for Science and Education ARS Research Program, MC-100-44 P.O. Box 117, Oak Ridge, TN 37831, USA.
Nucleic Acids Research
|May 5, 2016
Summary
SimpleSynteny is a new, user-friendly web platform for comparative genomics. It helps biologists assess gene synteny across multiple species, aiding evolutionary studies with easy-to-use tools.
Area of Science:
- Genomics
- Evolutionary Biology
- Bioinformatics
Background:
- Comparative genomics frequently defines syntenic relationships among orthologous gene clusters for organismal evolution studies.
- Next-generation sequencing has increased genome data availability, creating a need for accessible synteny assessment tools.
Purpose of the Study:
- To present SimpleSynteny, a novel web-based platform for interrogating genomic collinearity across multiple species.
- To provide a user-friendly pipeline for evaluating gene synteny in targeted comparative genomic analyses.
Main Methods:
- SimpleSynteny utilizes a web-based platform requiring only FASTA files of genomes and genes of interest.
- The platform guides users through an iterative process of genome customization and analysis.
- Includes tools for identifying gene targets within assemblies and optimizing circular genome analyses.
Main Results:
- SimpleSynteny enables direct interrogation of collinearity for local genomic neighbors across species.
- The iterative process allows customization of contig organization and integration of external knowledge.
- Facilitates high-resolution synteny figure generation.
Conclusions:
- SimpleSynteny offers a valuable, easy-to-use tool for comparative genomic analyses of gene synteny.
- The platform supports targeted evolutionary studies by simplifying the assessment of genomic relationships.
- Accessible via http://www.SimpleSynteny.com, it addresses the growing need for user-friendly synteny assessment tools.
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