View synteny among Rosaceae genomes using the new Tripal Synteny Viewer.
- Conserved syntenic regions among newest versions of publicly available Rosaceae genomes were analyzed by GDR and made available using the Tripal Synteny Viewer developed by the Fei Bioinformatics Lab from the Boyce Thomson Institute at Cornell University. Analysis was done using MCScanX (Wang et al. 2012) with default settings and blast files were made using blastp with an expectation value cutoff < 1e-10, maximum alignment of 5, and maximum scores of 5.
- The synteny viewer displays all the conserved syntenic blocks between a selected chromosome of a genome and another genome in a circular and tabular layout. Once a block is chosen in the circular or tabular layout, all the genes in the block are shown in a graphic and tabular format. The gene names have hyperlinks to gene pages where detailed information of the gene can be accessed. The ‘synteny’ section of the gene page displays all the orthologs and the paralogs with link to the corresponding syntenic blocks or gene pages.
Conserved syntenic regions among Rosaceae genomes were analyzed by GDR and made available using GBrowse_syn (McKay et al. 2010).
Analysis was done using i-ADHoRe v3.0 (Proost et al. 2012) with default settings. Gene homologs, identified using OrthoMCL program (Li et al. 2003), were used as an input for i-ADHoRe v3.0.
Analysis was done using Mercator (Dewey 2007) and Mavid (Bray and Pachter, 2004)