SyntTax protocols

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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 in pipeline

2016
PMCID: 4944035
PMID: 27446613
DOI: 10.1155/2016/4360285

[…] by jdet analysis (vide infra)., the mocrs of other species sharing ycze synteny with those retrieved from regprecise databank were collected from the syntax database (http://archaea.u-psud.fr/synttax/). indeed, presence of synteny is another strong hint of functional association between the regulator and the adjacent divergently transcribed gene []. the list of the yczr genes from syntax […]


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SyntTax in publications

 (14)
PMCID: 5770404
PMID: 29375530
DOI: 10.3389/fmicb.2017.02668

[…] for animal health and well-being and approved by the university of florida institutional animal care and use committee (iacuc)., 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 […]

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 )., sem showed that cells of strain s5.2 were 1.5–2.5 µm in length and 0.8–1.0 µm in width (additional file : figure […]

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

[…] large inversions of 139/143kb and 102/74kb respectively (). this relatively small number of inversions facilitated the investigation of the synteny breakpoints bordering both inversions. using the synttax web tool [], a composite representation was obtained as shown in . gene order is conserved immediately upstream and downstream of each inversion border and was used to identify the synteny […]

PMCID: 5253648
PMID: 28102223
DOI: 10.1038/ncomms14078

[…] that was 24 snps with 1 s.d. of 5 snps (). this translated to 8 snps per year, with a s.d. of 1.7 snps. we used this approximation to convert 3 snps to 4.5 months., we used the online version of synttax to compare the synteny of merc homologues within the xanthomonadales order., the genomic sequence data for the 576 s. maltophilia isolates have been deposited in the sequence read archive […]

PMCID: 4944223
PMID: 27185829
DOI: 10.1128/JB.00116-16

[…] (>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 (), the genome sequence data have been deposited in the european nucleotide archive under accession […]


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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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