HGTree


NAR Molecular Biology Database Collection entry number 1862
Jeong, Hyeon soo; Sung, Samsun; Kwon, Taehyung; Seo, Minseok; Caetano-Anolles, Kelsey; Choi, Sang Ho; Cho, Seoae; Nasir, Arshan; Kim, Heebal
1. Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak St. 599, Kwan-ak Gu, Seoul, 151-741, Republic of Korea
2. Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA
3. C&K genomics, Main Bldg. #514, SNU Research Park, Seoul 151-919, Republic of Korea
4. Department of Agricultural Biotechnology, Seoul National University, Seoul 151-742, Republic of Korea
5. 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
6. Department of Biosciences, COMSATS Institute of Information Technology, Park Road, Chak Shahzad, Islamabad 45550, Pakistan

Database Description

The HGTree database provides putative genome-wide horizontal gene transfer (HGT) information for 2,472 completely sequenced prokaryotic genomes. HGT detection is based on an explicit evolutionary model of tree reconstruction and relies on evaluating conflicts between phylogenetic tree of each orthologous gene set and corresponding 16S rRNA species tree. The database provides quick and easy access to HGT-related genes in hundreds of prokaryotic genomes and provides functionalities to detect HGT in user-customized datasets and gene and genome sequences. The database is freely available and can be easily scaled and updated to keep pace with the rapid rise in genomic information.

Acknowledgements

HGTree is funded by the Ministry of Food and Drug Safety [14162MFDS 972], republic of Korea. Thanks are also extended to the Higher Education Commission, Start-up Research Grant Program [Project No. 519], Pakistan. We are also grateful to Mukul Bansal and members of BIOPOP, Seoul National University and Functional Genomics Laboratory, COMSATS Institute of Information Technology, Islamabad for valuable comments and insightful discussions.

References

1. Kim K.M., Sung S., Caetano-Anollés G., Han J.Y., Kim H. An approach of orthology detection from homologous sequences under minimum evolution. Nucleic Acids Res. 2008;36:e110.
2. Price M.N., Dehal P.S., Arkin A.P. FastTree 2 - approximately maximum-likelihood trees for large alignments. PloS One 2010;5:e9490.
3. Bansal M.S., Alm E.J., Kellis M. Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss. Bioinformatics 2012;28:i283-i291.
4. Sievers F., Wilm A., Dineen D., Gibson T.J., Karplus K., Li W., Lopez R., McWilliam H., Remmert M., Söding J. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 2011;7:539.


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