SynChro: A Fast and Easy Tool to Reconstruct and Visualize Synteny Blocks along Eukaryotic Chromosomes

摘要: Reconstructing synteny blocks is an essential step in comparative genomics studies. Different methods were already developed to answer various needs such as genome (re-)annotation, identification of duplicated regions and whole duplication events or estimation rearrangement rates. We present SynChro, a tool that reconstructs between pairwise comparisons multiple genomes. SynChro based on simple algorithm computes Reciprocal Best-Hits (RBH) reconstruct the backbones then automatically completes these with non-RBH syntenic homologs. This approach has two main advantages: (i) block reconstruction fast (feasible desk computer for large eukaryotic genomes human) (ii) straightforward all steps are integrated (no need run Blast TribeMCL prior reconstruction) there only one parameter set up, stringency . Benchmarks three genomes, representing different levels conservation (Human/Mouse, Human/Zebra Finch Human/Zebrafish) show Synchro runs faster performs at least well other commonly used more sophisticated tools (MCScanX i-ADHoRe). In addition, provides user rich graphical outputs including dotplots, chromosome paintings detailed maps visualize homology relationships breakpoints included genetic features. freely available under BSD license http://www.lcqb.upmc.fr/CHROnicle/SynChro.html.