title: HGTree: database of horizontally transferred genes determined by tree reconciliation.
abstract: The HGTree database provides putative genome-wide horizontal gene transfer (HGT) information for 2472 completely sequenced prokaryotic genomes. This task is accomplished by reconstructing approximate maximum likelihood phylogenetic trees for each orthologous gene and corresponding 16S rRNA reference species sets and then reconciling the two trees under parsimony framework. The tree reconciliation method is generally considered to be a reliable way to detect HGT events but its practical use has remained limited because the method is computationally intensive and conceptually challenging. In this regard, HGTree (http://hgtree.snu.ac.kr) represents a useful addition to the biological community and enables quick and easy retrieval of information for HGT-acquired genes to better understand microbial taxonomy and evolution. The database is freely available and can be easily scaled and updated to keep pace with the rapid rise in genomic information.
authors.affiliation: Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak St. 599, Kwan-ak Gu, Seoul, 151-741, Republic of Korea Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA.
authors.forename: Hyeonsoo
authors.initials: H
authors.lastname: Jeong
authors.affiliation: C&K genomics, Main Bldg. #514, SNU Research Park, Seoul 151-919, Republic of Korea.
authors.forename: Samsun
authors.initials: S
authors.lastname: Sung
authors.affiliation: Department of Agricultural Biotechnology, Seoul National University, Seoul 151-742, Republic of Korea.
authors.forename: Taehyung
authors.initials: T
authors.lastname: Kwon
authors.affiliation: Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak St. 599, Kwan-ak Gu, Seoul, 151-741, Republic of Korea.
authors.forename: Minseok
authors.initials: M
authors.lastname: Seo
authors.affiliation: Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA.
authors.forename: Kelsey
authors.initials: K
authors.lastname: Caetano-Anollés
authors.affiliation: National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Seoul National University, Seoul 151-921, Republic of Korea.
authors.forename: Sang Ho
authors.initials: SH
authors.lastname: Choi
authors.affiliation: C&K genomics, Main Bldg. #514, SNU Research Park, Seoul 151-919, Republic of Korea.
authors.forename: Seoae
authors.initials: S
authors.lastname: Cho
authors.affiliation: Department of Biosciences, COMSATS Institute of Information Technology, Park Road, Chak Shahzad, Islamabad 45550, Pakistan arshan_nasir@comsats.edu.pk.
authors.forename: Arshan
authors.initials: A
authors.lastname: Nasir
authors.affiliation: Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak St. 599, Kwan-ak Gu, Seoul, 151-741, Republic of Korea Department of Agricultural Biotechnology, Seoul National University, Seoul 151-742, Republic of Korea heebal@snu.ac.kr.
authors.forename: Heebal
authors.initials: H
authors.lastname: Kim
mesh_terms: D030541:Databases, Genetic; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D019766:Genes, Archaeal; D005798:Genes, Bacterial; D064349:Genome, Microbial; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D012336:RNA, Ribosomal, 16S