| URL: | http://hgtree2.snu.ac.kr |
| Full name: | Database of Horizontally Transferred Genes Determined by Tree Reconciliation |
| Description: | HGTree v2.0 database provides you the genome-wide horizontal gene transfer information for 20,536 completely sequenced non-redundant prokaryotic genomes, and reliable HGT information results curated with various steps. HGTree v2.0 defines 4,017,521 HGT events by comparing the phylogenetic trees. |
| Year founded: | 2016 |
| Last update: | 2022 |
| Version: | v2.0 |
| Accessibility: |
Accessible
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| Country/Region: | Korea, Republic of |
| Data type: | |
| Data object: | |
| Database category: | |
| Major species: |
NA
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| Keywords: |
| University/Institution: | Seoul National University |
| Address: | Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea. |
| City: | Seoul |
| Province/State: | |
| Country/Region: | Korea, Republic of |
| Contact name (PI/Team): | Heebal Kim |
| Contact email (PI/Helpdesk): | heebal@snu.ac.kr |
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HGTree v2.0: a comprehensive database update for horizontal gene transfer (HGT) events detected by the tree-reconciliation method. [PMID: 36350646]
HGTree is a database that provides horizontal gene transfer (HGT) event information on 2472 prokaryote genomes using the tree-reconciliation method. HGTree was constructed in 2015, and a large number of prokaryotic genomes have been additionally published since then. To cope with the rapid rise of prokaryotic genome data, we present HGTree v2.0 (http://hgtree2.snu.ac.kr), a newly updated version of our HGT database with much more extensive data, including a total of 20 536 completely sequenced non-redundant prokaryotic genomes, and more reliable HGT information results curated with various steps. As a result, HGTree v2.0 has a set of expanded data results of 6 361 199 putative horizontally transferred genes integrated with additional functional information such as the KEGG pathway, virulence factors and antimicrobial resistance. Furthermore, various visualization tools in the HGTree v2.0 database website provide intuitive biological insights, allowing the users to investigate their genomes of interest. |
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HGTree: database of horizontally transferred genes determined by tree reconciliation. [PMID: 26578597]
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. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. |