title: SimpleSynteny: a web-based tool for visualization of microsynteny across multiple species.
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.
authors.affiliation: Systematic 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.
authors.forename: Daniel
authors.identifier: 0000-0002-6101-6693
authors.initials: D
authors.lastname: Veltri
authors.affiliation: Systematic Mycology and Microbiology Laboratory, U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), 10300 Baltimore Avenue, Building 10A, Beltsville, MD 20705, USA.
authors.forename: Martha Malapi
authors.initials: MM
authors.lastname: Wight
authors.affiliation: Systematic Mycology and Microbiology Laboratory, U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), 10300 Baltimore Avenue, Building 10A, Beltsville, MD 20705, USA joanne.crouch@ars.usda.gov.
authors.forename: Jo Anne
authors.initials: JA
authors.lastname: Crouch
mesh_terms: D000465:Algorithms; D001230:Aspergillus / Q000145:classification / Q000235:genetics; D020231:Colletotrichum / Q000145:classification / Q000235:genetics; D003196:Computer Graphics; D020451:Contig Mapping; D005670:Fusarium / Q000145:classification / Q000235:genetics; D016681:Genome, Fungal; D059014:High-Throughput Nucleotide Sequencing; D016247:Information Storage and Retrieval; D020407:Internet; D010935:Plant Diseases / Q000382:microbiology; D017422:Sequence Analysis, DNA; D026801:Synteny; D014242:Trichoderma / Q000145:classification / Q000235:genetics; D014584:User-Computer Interface