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GOHTAM: a Website for 'Genomic Origin of Horizontal Transfers, Alignment and Metagenomics'

Overview
Journal Bioinformatics
Publisher Oxford University Press
Specialty Biology
Date 2012 Mar 20
PMID 22426345
Citations 19
Authors
Sabine Menigaud
Ludovic Mallet
Geraldine Picord
Cecile Churlaud
Alexandre Borrel
Patrick Deschavanne
Affiliations
Soon will be listed here.
Abstract

Motivation: This website allows the detection of horizontal transfers based on a combination of parametric methods and proposes an origin by researching neighbors in a bank of genomic signatures. This bank is also used to research an origin to DNA fragments from metagenomics studies.

Results: Different services are provided like the possibility of inferring a phylogenetic tree with sequence signatures or comparing two genomes and displaying the rearrangements that happened since their separation.

Availability And Implementation: http://gohtam.rpbs.univ-paris-diderot.fr/

Citing Articles

Metagenomic Mining for Esterases in the Microbial Community of Los Rueldos Acid Mine Drainage Formation.

Vidal P, Martinez-Martinez M, Fernandez-Lopez L, Roda S, Mendez-Garcia C, Golyshina O Front Microbiol. 2022; 13:868839.

PMID: 35663881 PMC: 9162777. DOI: 10.3389/fmicb.2022.868839.

ShadowCaster: Compositional Methods under the Shadow of Phylogenetic Models to Detect Horizontal Gene Transfers in Prokaryotes.

Sanchez-Soto D, Aguero-Chapin G, Armijos-Jaramillo V, Perez-Castillo Y, Tejera E, Antunes A Genes (Basel). 2020; 11(7).

PMID: 32645885 PMC: 7397055. DOI: 10.3390/genes11070756.

Bioprospecting Reveals Class III ω-Transaminases Converting Bulky Ketones and Environmentally Relevant Polyamines.

Coscolin C, Katzke N, Garcia-Moyano A, Navarro-Fernandez J, Almendral D, Martinez-Martinez M Appl Environ Microbiol. 2018; 85(2).

PMID: 30413473 PMC: 6328768. DOI: 10.1128/AEM.02404-18.

Horizontal acquisition of a hypoxia-responsive molybdenum cofactor biosynthesis pathway contributed to Mycobacterium tuberculosis pathoadaptation.

Levillain F, Poquet Y, Mallet L, Mazeres S, Marceau M, Brosch R PLoS Pathog. 2017; 13(11):e1006752.

PMID: 29176894 PMC: 5720804. DOI: 10.1371/journal.ppat.1006752.

PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies.

Mallet L, Bitard-Feildel T, Cerutti F, Chiapello H Bioinformatics. 2017; 33(20):3283-3285.

PMID: 28637232 PMC: 5860033. DOI: 10.1093/bioinformatics/btx396.

References
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