title: LCGserver: A Webserver for Exploring Evolutionary Trajectory of Gene Orders in a Large Number of Genomes.
abstract: Genes and chromosomes are highly organized; together with protein-coding sequence, gene structure at per gene level and gene order at cluster level are both variable in a context of lineages and under natural selection. How gene order and chromosome organization are related and selected remains to be illuminated. The number of newly-sequenced genomes from various taxa has been increasing rapidly, but there have not been easy-to-use web tools that allow better visualization for gene order in a large genome collection. Here, we describe a webserver, LCGserver (http://lcgbase.big.ac.cn/LCGserver/), for exploring evolutionary dynamics of gene orders over diverse lineages. This server provides gene order information at three levels: single gene, paired gene (a minimal cluster), and clustered gene (more than two genes). The most exclusive feature of LCGserver is alignment and visualization of neighboring genes based on orthology, allowing users to inspect all conserved and dynamic events of gene order along chromosomes in a lineage-specific manner. In addition, it categories paired genes into six patterns and identifies fully-conserved gene clusters within and among lineages.
authors.affiliation: 1 CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics , Chinese Academy of Sciences, Beijing, People's Republic of China .|2 Stem Cell Laboratory, UCL Cancer Institute, University College London , London, United Kingdom .
authors.forename: Dapeng
authors.initials: D
authors.lastname: Wang
authors.affiliation: 1 CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics , Chinese Academy of Sciences, Beijing, People's Republic of China .
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
mesh_terms: D005075:Biological Evolution; D002874:Chromosome Mapping; D023061:Gene Order / Q000235:genetics*; D005810:Multigene Family; D016415:Sequence Alignment