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Repository synteny_mapper
Name: synteny_mapper
Owner: s-kaufmann
Synopsis: A tool for finding microrearrangements within syntenic regions, visualization thereof and comparison of (UCSC) feature tracks between two species
SyntenyMapper provides the user with the functionality of refining syntenic regions (e.g. by ENSEMBL) by finding all microrearrangements within. It visualizes the gene rearrangements and generates a one-to-one map of orthologs between two species as well as a list of regions with conserved gene order. Comparison of genes' features between species is also possible based on this mapping.
Link to this repository: https://toolshed.g2.bx.psu.edu/view/s-kaufmann/synteny_mapper/1fdfbe87a959
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/s-kaufmann/synteny_mapper
Type: unrestricted
Revision: 25:1fdfbe87a959
This revision can be installed: True
Times cloned / installed: 218
Dependencies of this repository

Tool dependencies - repository tools require handling of these dependencies
Name Version Type
R_3_0_2 3.0.2 package
circos 0.64 package
JAR_PATH set_environment
CIRCOS_SCRIPT_PATH set_environment
R_PATH set_environment

Contents of this repository

Valid tools - click the name to preview the tool and use the pop-up menu to inspect all metadata
Name Description Version Minimum Galaxy Version
Compares tracks in .bed-format between two species based on the synteny-based mapping 1.0.0 any
Maps maximum stretches of orthologous genes with conserved order within large synteny regions 1.0.0 any
Visualizes micro-rearrangements for one synteny region 1.0.0 any

Categories
Sequence Analysis - Tools for performing Protein and DNA/RNA analysis