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Protocols

[email protected] specifications

Information


Unique identifier OMICS_05996
Name [email protected]
Alternative name Mobyle
Interface Web user interface
Restrictions to use None
License GNU General Public License version 2.0
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Catherine Letondal

Publication for [email protected]

[email protected] citations

 (223)
library_books

Evolution of Synonymous Codon Usage Bias in West African and Central African Strains of Monkeypox Virus

2018
Evol Bioinform Online
PMCID: 5846927
PMID: 29551886
DOI: 10.1177/1176934318761368

[…] ata., The Mann-Whitney 2-sample test was used to analyze the intergenomic differences in the ENC values. PAST software version 2.12 was used for the Spearman rank correlation analysis. CodonW (http://mobyle.pasteur.fr/cgi-bin/portal.py?#forms::codonw) was used to compute the values of the ENC, hydrophobicity, and aromaticity. MEGA version 5.2.2 was used to calculate the compositions of the nucleot […]

call_split

NS2 proteases from hepatitis C virus and related hepaciviruses share composite active sites and previously unrecognized intrinsic proteolytic activities

2018
PLoS Pathog
PMCID: 5819835
PMID: 29415072
DOI: 10.1371/journal.ppat.1006863
call_split See protocol

[…] age sites using the SignalP 4.0 server (http://www.cbs.dtu.dk/services/SignalP/) and examining sequence homology with HCV and GBV-B polyproteins. Protein sequence analyses were performed by using the Mobyle portal for bioinformatics analyses (http://mobyle.pasteur.fr/) []. Multiple sequence alignments were performed with the T-coffee multiple sequence alignment program [] using the corresponding w […]

library_books

A eukaryotic nicotinate inducible gene cluster: convergent evolution in fungi and bacteria

2017
Open Biol
PMCID: 5746545
PMID: 29212709
DOI: 10.1098/rsob.170199

[…] S-i and MAFFT G-INS-i); colour labelling of alignments was done with BoxShade (http://www.ch.embnet.org/software/BOX_form.html). Alignment curation for phylogeny was carried out with BMGE 1.0 (http://mobyle.pasteur.fr/cgi-bin/portal.py#forms::BMGE) [] and maximum-likelihood phylogeny with PhyML 3.0 with automatic model selection (LG substitution model selected) [,] indicating approximate likelihoo […]

library_books

Analysis of the codon usage pattern in Middle East Respiratory Syndrome Coronavirus

2017
Oncotarget
PMCID: 5746386
PMID: 29299151
DOI: 10.18632/oncotarget.22738

[…] 2s%, GC3s%) was calculated using the cusp program online (http://emboss.toulouse.inra.fr/cgi-bin/emboss/cusp). The A3s, U3s, G3s, GC% and GC3s were calculated using the Codon W program online (http://mobyle.pasteur.fr/cgi-bin/portal.py?#forms::CodonW). […]

library_books

Insights into soybean transcriptome reconfiguration under hypoxic stress: Functional, regulatory, structural, and compositional characterization

2017
PLoS One
PMCID: 5690659
PMID: 29145496
DOI: 10.1371/journal.pone.0187920

[…] athways of DEGs related to amino acids and its derivatives were analyzed using KEGG Mapper—Search&Color Pathway []. The Relative Synonymous Codon Usage (RSCU) was calculated with CodonW 1.4.4 (http://mobyle.pasteur.fr/cgi-bin/portal.py?#forms::CodonW). The copy numbers of soybean nuclear tRNA genes was extracted from the genomic tRNA database (http://gtrnadb.ucsc.edu/) []. Samples sizes used for s […]

library_books

Characterization of ecologically diverse viruses infecting co occurring strains of cosmopolitan hyperhalophilic Bacteroidetes

2017
PMCID: 5776456
PMID: 29099492
DOI: 10.1038/ismej.2017.175

[…] dogram reconstructed using the UPGMA clustering method implemented in the bioinformatic package Geneious 8.1.6. To determine the tetranucleotide frequency of the isolates, the web-based analysis site Mobyle portal was used. These results were compared by principal component analysis, (IBM SPSS Statistics v.22, Armonk, NY, USA) with the tetranucleotide frequencies found in virus genomes cloned dire […]

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[email protected] institution(s)
Groupe Logiciels et Banques de Données, Institut Pasteur, Paris, France

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