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SimpleSynteny

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A 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. The standard pipeline for SimpleSynteny consists of three primary steps: (1) data input, (2) contig editing and (3) customization of graphical output. 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.

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SimpleSynteny forum

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SimpleSynteny classification

SimpleSynteny specifications

Interface:
Web user interface
Input data:
Genome or gene
Computer skills:
Basic
Stability:
Stable
Restrictions to use:
None
Input format:
FASTA
Version:
1.1
Maintained:
Yes

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SimpleSynteny classification

SimpleSynteny specifications

Software type:
Pipeline/Workflow
Restrictions to use:
None
Input format:
FASTA
Computer skills:
Advanced
Stability:
Stable
Interface:
Command line interface
Input data:
Genome or gene
Operating system:
Unix/Linux
Version:
1.1
Maintained:
Yes

SimpleSynteny distribution

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SimpleSynteny support

Maintainer

  • Jo Anne Crouch <>
  • Jo Anne Crouch <>

Credits

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Publications

Institution(s)

Systematic Mycology and Microbiology Laboratory, US Department of Agriculture (USDA), Agricultural Research Service (ARS), Beltsville, MD, USA; Oak Ridge Institute for Science and Education ARS Research Program, Oak Ridge, TN, USA

Funding source(s)

2013-2015 United States Department of Agriculture (USDA)—Animal and Plant Health Inspection Service Farm Bill 10201 and 10007 Program funds; USDA—Agricultural Research Service (ARS) [project 8042-22000-279-00D]; USDA-ARS Floriculture and Nursery Research Initiative [project 0500-00059-001]. Inter-agency fellowship agreement between the United States Department of Energy (DOE) and the USDA through the Oak Ridge Institute for Science and Education ARS Research Participation Program Fellowship [DOE contract DE-AC05-06OR23100]; Class of 2013 USDA-ARS Headquarters Research Associate Award

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