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Protocols

SyntTax specifications

Information


Unique identifier OMICS_17868
Name SyntTax
Interface Web user interface
Restrictions to use None
Input data A protein sequence.
Input format FASTA
Programming languages C#, Javascript, Other
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Jacques Oberto

Publication for SyntTax

SyntTax citations

 (17)
library_books

Production of the Plant Hormone Auxin by Salmonella and Its Role in the Interactions with Plants and Animals

2018
Front Microbiol
PMCID: 5770404
PMID: 29375530
DOI: 10.3389/fmicb.2017.02668

[…] Synteny analysis was carried out using default parameters in the SyntTax web server (Oberto, ). Sequences were imported from GenBank. UV peak integration was conducted with proprietary Waters software, and analysis of mass spectral data was carried out using Thermo […]

library_books

A novel Porphyromonas gingivalis enzyme: An atypical dipeptidyl peptidase III with an ARM repeat domain

2017
PLoS One
PMCID: 5708649
PMID: 29190734
DOI: 10.1371/journal.pone.0188915

[…] in Database, February 2017, []). In Bacteroides and Prevotella genomes, on the other hand, we found these domains in close proximity, in the same order as in Porphyromonas, but as two separate genes (SyntTax, February 2017, http://archaea.u-psud.fr/synttax/). […]

library_books

Phenotypic and genomic survey on organic acid utilization profile of Pseudomonas mendocina strain S5.2, a vineyard soil isolate

2017
PMCID: 5484659
PMID: 28655216
DOI: 10.1186/s13568-017-0437-7

[…] JSpeciesWS (http://jspecies.ribohost.com/jspeciesws/) with above cutoff more than 95% (Richter et al. ). Lastly, the synteny and comparative analysis on the genes of interest were conducted based on SyntTax web server using default parameter followed by manual verification (Oberto ). […]

library_books

Flipping chromosomes in deep sea archaea

2017
PLoS Genet
PMCID: 5495485
PMID: 28628615
DOI: 10.1371/journal.pgen.1006847

[…] Genomic sequences were compared and aligned by dotplot analysis using Gepard []. Conservation of gene order was assessed by synteny analysis using Absynte [] and SyntTax []. The original genome of Thermococcus 5–4 JCM31817 (GenBank accession CP021848) and the genomes of sub-cultured T. nautili 60G and 66G and T. sp. 5–4 36G and 66G were sequenced by Genoscope […]

library_books

Global and local selection acting on the pathogen Stenotrophomonas maltophilia in the human lung

2017
Nat Commun
PMCID: 5253648
PMID: 28102223
DOI: 10.1038/ncomms14078

[…] We used the online version of SyntTax to compare the synteny of merC homologues within the Xanthomonadales order. […]

call_split

Identification of a Lipoteichoic Acid Glycosyltransferase Enzyme Reveals that GW Domain Containing Proteins Can Be Retained in the Cell Wall of Listeria monocytogenes in the Absence of Lipoteichoic Acid or Its Modifications

2016
J Bacteriol
PMCID: 4944223
PMID: 27185829
DOI: 10.1128/JB.00116-16
call_split See protocol

[…] high-frequency (>85%) changes are listed in Table S3 for the different strains. To determine the conservation of the gtlA gene among other Listeria species, a synteny analysis was performed using the SyntTax web server (http://archaea.u-psud.fr/synttax/) and all available sequenced Listeria genomes () […]

Citations

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SyntTax institution(s)
Université Paris-Sud 11, CNRS, Institut de Génétique et Microbiologie, Orsay, France
SyntTax funding source(s)
This work was supported by the “Centre National pour la Recherche Scientifique” (CNRS) and the "Agence Nationale de la Recherche" (ANR GRONAG grant).

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