HGTector statistics

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Citations per year

Number of citations per year for the bioinformatics software tool HGTector
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Tool usage distribution map

This map represents all the scientific publications referring to HGTector per scientific context
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Protocols

HGTector specifications

Information


Unique identifier OMICS_23772
Name HGTector
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl
License BSD 2-clause “Simplified” License
Computer skills Medium
Version 0.2.2
Stability Stable
Maintained Yes

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Versioning


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Documentation


Maintainers


  • person_outline Qiyun Zhu
  • person_outline Katharina Dittmar

Publication for HGTector

HGTector citations

 (13)
library_books

The Swinholide Biosynthesis Gene Cluster from a Terrestrial Cyanobacterium, Nostoc sp. Strain UHCC 0450

2018
Appl Environ Microbiol
PMCID: 5772238
PMID: 29150506
DOI: 10.1128/AEM.02321-17

[…] To detect the presence of HGT, we used two different approaches previously suggested to be clear-cut and reliable (, ). First, we relied on a phylogeny-informed BLAST-based analysis implemented in HGTector version 0.2.0 (). The self-group was defined manually for each analysis, and each threshold cutoff was determined as suggested by the kernel density function for the definition of close and d […]

library_books

The Composite 259 kb Plasmid of Martelella mediterranea DSM 17316T–A Natural Replicon with Functional RepABC Modules from Rhodobacteraceae and Rhizobiaceae

2017
Front Microbiol
PMCID: 5613091
PMID: 28983283
DOI: 10.3389/fmicb.2017.01787

[…] HGT analysis of M. mediterranea DSM 17316T plasmids was conducted using HGTector.py (Zhu et al., ) with BLASTP against the NCBI non-redundant (nr) sequence database (download: October, 12th 2016), the taxonDMP (October, 12th 2016) and release 78 of MultispeciesAutonomousP […]

library_books

Genomic insights into temperature dependent transcriptional responses of Kosmotoga olearia, a deep biosphere bacterium that can grow from 20 to 79 °C

2017
Extremophiles
PMCID: 5674127
PMID: 28894932
DOI: 10.1007/s00792-017-0956-9

[…] Obtaining “pre-adapted” genes from other genomes is one way prokaryotes adjust to new environmental conditions (Boucher et al. ). Using HGTector (Zhu et al. ) we predicted that 354 of K. olearia’s 2118 protein-coding genes have been acquired laterally by K. olearia or the Kosmotogales (i.e., Kosmotoga and Mesotoga genera), presumably […]

library_books

Analysis of the genome sequence of Phomopsis longicolla: a fungal pathogen causing Phomopsis seed decay in soybean

2017
BMC Genomics
PMCID: 5584002
PMID: 28870170
DOI: 10.1186/s12864-017-4075-x

[…] To identify putatively horizontally transferred genes in the P. longicolla isolate MSPL 10–6, the HGTector software (http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-717) was used, which follows a hybrid approach between “BLAST-based” and phylogenetic. The software was setup with […]

library_books

Horizontally Acquired Biosynthesis Genes Boost Coxiella burnetii's Physiology

2017
PMCID: 5423948
PMID: 28540258
DOI: 10.3389/fcimb.2017.00174

[…] only three other bacteria within the order Legionellales—Legionella, Rickettsiella, and Diplorickettsia. In order to circumvent this limitation, we utilized a phylogeny informed BLAST-based approach (HGTector, Zhu et al., ), but applied very strict criteria to categorize a gene as horizontally acquired. We set Coxiella as the self-group, and Legionellales as the exclusion group, which captured HGT […]

library_books

Genomic characterization of Nontuberculous Mycobacteria

2017
Sci Rep
PMCID: 5366915
PMID: 28345639
DOI: 10.1038/srep45258

[…] In order to determine which genes were potentially acquired through LGT a homology/taxonomy approach was employed using HGTector v0.1.8. This analysis pipeline compares protein sequences (labelled the self set) to a database of potential donors and assesses whether there is a higher abundance of closely related sequenc […]


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HGTector institution(s)
Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA; Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, USA
HGTector funding source(s)
Supported by NSF DEB 1213740.

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