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HGT-DB specifications

Information


Unique identifier OMICS_03191
Name HGT-DB
Alternative name Horizontal Gene Transfer DataBase
Restrictions to use None
Maintained Yes

Publication for Horizontal Gene Transfer DataBase

HGT-DB citations

 (6)
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Complete Genome Analysis of Three Acinetobacter baumannii Clinical Isolates in China for Insight into the Diversification of Drug Resistance Elements

2013
PLoS One
PMCID: 3691203
PMID: 23826102
DOI: 10.1371/journal.pone.0066584
call_split See protocol

[…] were identified by using Ori-Finder . The regions with abnormal G+C contents in the genomic sequence were obtained by using the GC-Profile program to identify the genomic islands and screened in the horizontal gene transfer database (HGT-DB) . […]

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Phylogenomic Evidence for a Myxococcal Contribution to the Mitochondrial Fatty Acid Beta Oxidation

2011
PLoS One
PMCID: 3131387
PMID: 21760940
DOI: 10.1371/journal.pone.0021989
call_split See protocol

[…] ethods: (i) Karlin's method based on determined codon usage and calculated using software available from the Computational Microbiology Laboratory (http://www.cmbl.uga.edu/software.html) , , (ii) the Horizontal Gene Transfer Database (HGT-DB), which relies on G+C content, codon usage, gene position and amino acid content (http://genomes.urv.es/HGT-DB/) , and (iii) the Island Viewer server to ident […]

library_books

Reconstructing genome trees of prokaryotes using overlapping genes

2010
BMC Bioinformatics
PMCID: 2845580
PMID: 20181237
DOI: 10.1186/1471-2105-11-102

[…] and other Proteobacteria, if all these CDSs in W. brevipalpisa are excluded from our analysis in this study. Instead, we first removed those horizontally transferred genes currently annotated at the HGT-DB database [] and then used the BBH approach, as mentioned previously, to identify putative orthologous genes by setting the parameters with a minimum E-value of 10-8, at least 85% of each authen […]

library_books

The impact of the neisserial DNA uptake sequences on genome evolution and stability

2008
Genome Biol
PMCID: 2397512
PMID: 18366792
DOI: 10.1186/gb-2008-9-3-r60

[…] ity in genomes, we were surprised to discover that predicted horizontally transferred regions contain very few DUSs. Laterally acquired genes of N. meningitidis Z2491 and MC58 were collected from the HGT-DB database [] and scanned for the presence of DUSs. These predicted recently transferred genes with low %G+C amounted to 5.6% of the Z2491 genome and 7.1% of the MC58 genome, but they contained o […]

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Detecting laterally transferred genes: use of entropic clustering methods and genome position

2007
Nucleic Acids Res
PMCID: 1950545
PMID: 17591616
DOI: 10.1093/nar/gkm204
call_split See protocol

[…] mple size and n0 is the tuning parameter ()]. Garcia-Vallve et al. () used multiple metrics, namely G+C content, codon and amino acid usage to compile putative horizontally transferred genes in their HGT-DB database. The machine-learning method Wn-SVM uses a one-class support vector machine for identifying alien genes (). Alien-Hunter detects putative alien genes using variable order motif distrib […]

library_books

An acquisition account of genomic islands based on genome signature comparisons

2005
BMC Genomics
PMCID: 1310630
PMID: 16297239
DOI: 10.1186/1471-2164-6-163

[…] regard to codon usage and GC content as well as dinucleotide composition. Both chromosomes of V. vulnificus CMCP6 contain a large number of GIs as identified by Garcia-Vallve and co-workers. In their Horizontal Gene Transfer Database (HGT-DB) 10 and 11 large (>10 kbp) putatively horizontally acquired gene clusters are described for V. vulnificus CMCP6 chromosome I and chromosome II, respectively. […]

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HGT-DB institution(s)
Evolutionary Genomics Group, Biochemistry and Biotechnology Department, Rovira i Virgili University, Tarragona, Spain

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