SynChro: a fast and easy tool to reconstruct and visualize synteny blocks along eukaryotic chromosomes.

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 genome duplication events or estimation of rearrangement rates. We prese...

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Autores principales:	Guénola Drillon, Alessandra Carbone, Gilles Fischer
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/a33fdd96c2994c96b6ea219b5cb4014c
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spelling	oai:doaj.org-article:a33fdd96c2994c96b6ea219b5cb4014c2021-11-18T08:27:06ZSynChro: a fast and easy tool to reconstruct and visualize synteny blocks along eukaryotic chromosomes.1932-620310.1371/journal.pone.0092621https://doaj.org/article/a33fdd96c2994c96b6ea219b5cb4014c2014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24651407/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Reconstructing 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 genome duplication events or estimation of rearrangement rates. We present SynChro, a tool that reconstructs synteny blocks between pairwise comparisons of multiple genomes. SynChro is based on a simple algorithm that computes Reciprocal Best-Hits (RBH) to reconstruct the backbones of the synteny blocks and then automatically completes these blocks with non-RBH syntenic homologs. This approach has two main advantages: (i) synteny block reconstruction is fast (feasible on a desk computer for large eukaryotic genomes such as human) and (ii) synteny block reconstruction is straightforward as all steps are integrated (no need to run Blast or TribeMCL prior to reconstruction) and there is only one parameter to set up, the synteny block stringency [Formula: see text]. Benchmarks on three pairwise comparisons of genomes, representing three different levels of synteny conservation (Human/Mouse, Human/Zebra Finch and Human/Zebrafish) show that Synchro runs faster and performs at least as well as two other commonly used and more sophisticated tools (MCScanX and i-ADHoRe). In addition, SynChro provides the user with a rich set of graphical outputs including dotplots, chromosome paintings and detailed synteny maps to visualize synteny blocks with all homology relationships and synteny breakpoints with all included genetic features. SynChro is freely available under the BSD license at http://www.lcqb.upmc.fr/CHROnicle/SynChro.html.Guénola DrillonAlessandra CarboneGilles FischerPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 3, p e92621 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Guénola Drillon Alessandra Carbone Gilles Fischer SynChro: a fast and easy tool to reconstruct and visualize synteny blocks along eukaryotic chromosomes.
description	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 genome duplication events or estimation of rearrangement rates. We present SynChro, a tool that reconstructs synteny blocks between pairwise comparisons of multiple genomes. SynChro is based on a simple algorithm that computes Reciprocal Best-Hits (RBH) to reconstruct the backbones of the synteny blocks and then automatically completes these blocks with non-RBH syntenic homologs. This approach has two main advantages: (i) synteny block reconstruction is fast (feasible on a desk computer for large eukaryotic genomes such as human) and (ii) synteny block reconstruction is straightforward as all steps are integrated (no need to run Blast or TribeMCL prior to reconstruction) and there is only one parameter to set up, the synteny block stringency [Formula: see text]. Benchmarks on three pairwise comparisons of genomes, representing three different levels of synteny conservation (Human/Mouse, Human/Zebra Finch and Human/Zebrafish) show that Synchro runs faster and performs at least as well as two other commonly used and more sophisticated tools (MCScanX and i-ADHoRe). In addition, SynChro provides the user with a rich set of graphical outputs including dotplots, chromosome paintings and detailed synteny maps to visualize synteny blocks with all homology relationships and synteny breakpoints with all included genetic features. SynChro is freely available under the BSD license at http://www.lcqb.upmc.fr/CHROnicle/SynChro.html.
format	article
author	Guénola Drillon Alessandra Carbone Gilles Fischer
author_facet	Guénola Drillon Alessandra Carbone Gilles Fischer
author_sort	Guénola Drillon
title	SynChro: a fast and easy tool to reconstruct and visualize synteny blocks along eukaryotic chromosomes.
title_short	SynChro: a fast and easy tool to reconstruct and visualize synteny blocks along eukaryotic chromosomes.
title_full	SynChro: a fast and easy tool to reconstruct and visualize synteny blocks along eukaryotic chromosomes.
title_fullStr	SynChro: a fast and easy tool to reconstruct and visualize synteny blocks along eukaryotic chromosomes.
title_full_unstemmed	SynChro: a fast and easy tool to reconstruct and visualize synteny blocks along eukaryotic chromosomes.
title_sort	synchro: a fast and easy tool to reconstruct and visualize synteny blocks along eukaryotic chromosomes.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/a33fdd96c2994c96b6ea219b5cb4014c
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SynChro: a fast and easy tool to reconstruct and visualize synteny blocks along eukaryotic chromosomes.

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