SynTView protocols

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SynTView specifications

Information


Unique identifier OMICS_01500
Name SynTView
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Stability Stable
Requirements
AdobeW Flash Player
Maintained Yes

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Documentation


Maintainer


  • person_outline Pierre Lechat <>

Additional information


http://hub18.hosting.pasteur.fr/SynTView/GetStarted/ http://hub18.hosting.pasteur.fr/SynTView/documentation/

Publication for SynTView

SynTView in pipelines

 (2)
2016
PMCID: 4752609
PMID: 26884428
DOI: 10.1128/mBio.02183-15

[…] stringent filter were regarded as true positives and were searched for in the original set for every strain in which they had been filtered out. snps, short indels, and coverage were visualized with syntview (). specific analysis of clones from the main french lineage was done by manually checking read alignments around snps with tablet (). four regions corresponding to mges not present […]

2014
PMCID: 3977354
PMID: 24667708
DOI: 10.1128/mBio.00969-14

[…] 10403s, and the sequence was submitted to the ena database (accession number hg421741). interactive visualization of the syntenic organization of listeria genomes is available with the flash-based syntview () software available at http://genopole.pasteur.fr/syntview/flash/listeria_monocytogenes/synwebegd_final.html., bacterial overnight cultures were diluted in bhi, and bacteria were grown […]

SynTView in publications

 (7)
PMCID: 5006051
PMID: 27577684
DOI: 10.1038/srep32252

[…] we defined an orthologous couple when both blastp p values were below 10−5. the positions of orthologous genes in c. neoformans var. neoformans and c. neoformans var. grubii were visualized using syntview. the full alignment can be obtained at http://genopole.pasteur.fr/syntview/flash/cryptococcus_neoformans_grubii_h99/synweb.html., in order to identify protein families, we performed protein […]

PMCID: 4943205
PMID: 27371955
DOI: 10.1093/gbe/evw140

[…] 10−20. all amino acid sequences were validated for the presence of expected domains by pfam., interactive visualization of the syntenic organization of the leishmania genomes was performed using the syntview web tool (). results are publicly available via a web interface at the following url http://genopole.pasteur.fr/syntview/flash/leishmania/synweb.html (last accessed june 18, 2016) for four […]

PMCID: 4752609
PMID: 26884428
DOI: 10.1128/mBio.02183-15

[…] stringent filter were regarded as true positives and were searched for in the original set for every strain in which they had been filtered out. snps, short indels, and coverage were visualized with syntview (). specific analysis of clones from the main french lineage was done by manually checking read alignments around snps with tablet (). four regions corresponding to mges not present […]

PMCID: 4586476
PMID: 26389958
DOI: 10.3390/vaccines3030751

[…] and snps detection was done using galaxy platform (clc assembly cell v4.2 (clc bio, aarhus, denmark); snpeff (http://snpeff.sourceforge.net/snpeff.html#citing). snps were concatenated using syntview (http://genopole.pasteur.fr/syntview/), alignment was done using multalin (http://multalin.toulouse.inra.fr/multalin/) and the phylogenetic tree was constructed using quicktree […]

PMCID: 4374582
PMID: 25815061
DOI: 10.1186/s13040-015-0045-5

[…] dimension reduction to 2d or 3d space, such as principal components analysis (pca) or multidimensional scaling (mds)., at the moment, a number of tools exist for visualization of metagenomic data: syntview [], metasee [], metaphlan [] and others, most of them are concentrated on community profiling and use the phylogenetic information for visualizing relationship between otus. […]

SynTView institution(s)
Institut Pasteur, Plate-forme Bioanalyse Génomique, Paris, France
SynTView funding source(s)
Supported by Institut Pasteur and grants from the Région Ile-de-France (DIM Malinf), the Agence Nationale de la Recherche (ANR-08-GENM-027) and the French Government’s Investissements d’Avenir program (Laboratoire d’Excellence “Integrative Biology of Emerging Infectious Diseases” - ANR-10-LABX-62-IBEID).

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