FIGENIX protocols

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FIGENIX specifications

Information


Unique identifier OMICS_25134
Name FIGENIX
Interface Web user interface
Restrictions to use Academic or non-commercial use
Computer skills Basic
Maintained No

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Publication for FIGENIX

FIGENIX in pipelines

 (3)
2012
PMCID: 3418167
PMID: 22904610
DOI: 10.4137/EBO.S9186

[…] in biological ontologies. the ontological database model scheme is described in., all the phylogenetic trees present in the database were built automatically using the software platform figenix, driven by the dagobah expert system. dagobah is a multi-agent system in which specific agents have been developed for genetic event detection and verification. the phylogenetic trees […]

2010
PMCID: 2978717
PMID: 21085602
DOI: 10.1371/journal.pone.0015506

[…] the protein domain structure of nme proteins was obtained from the genbank conserved domain database ., phylogenetic reconstructions were performed using the automated genomic annotation platform figenix . for each phylogenetic tree reconstruction, all selected protein sequences were added to a single multiple sequence alignment. sequence alignment was performed automatically by the figenix […]

2006
PMCID: 1660568
PMID: 17092334
DOI: 10.1186/1471-2148-6-92

[…] families in order to analyse and further characterise the general trends underpinning these connections., phylogenetic analyses were performed using the automated genomic annotation platform figenix [] to retrieve sequences and alignments and perform phylogenetic reconstruction. the pipeline used applied three different methods of phylogenetic tree reconstruction, i.e. maximum parsimony […]


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FIGENIX in publications

 (30)
PMCID: 5913061
PMID: 29692905
DOI: 10.1016/j.nmni.2018.01.003

[…] than 1e-05 for orfs with sequence length <80 aa). such parameter thresholds have been used in previous studies to define orfans. the annotation process was performed using dagobah including the figenix libraries, which provided the pipeline analysis., sequences were recovered after a nucleotide blast against the 16s rrna database of the all-species living tree silva project (ltps119). […]

PMCID: 5751998
PMID: 29321938
DOI: 10.1016/j.nmni.2017.11.009

[…] dsm 17679, bacteroides fluxus yit 12057 and bacteroides rodentium jcm 16496. annotation and comparison processes were performed by the multiagent software system dagobah , which includes figenix libraries that provided pipeline analysis. we also performed genome-to-genome distance calculator (ggdc) analysis using the ggdc web server, as previously reported , ., strain […]

PMCID: 5583396
PMID: 28912952
DOI: 10.1016/j.nmni.2017.07.004

[…] predicted genes according to the cogs of proteins (same method as for the genome annotation). annotation and comparison processes were performed by the multi-agent software system dagobah including figenix libraries to provide pipeline analysis , . finally, to evaluate the genomic similarity between studied genomes, two main parameters, digital dna-dna hybridization (dddh)—which exhibits a high […]

PMCID: 5496451
PMID: 28706723
DOI: 10.1016/j.nmni.2017.04.005

[…] according to the cogs of proteins (using the same method as for the genome annotation). annotation and comparison processes were performed by the multiagent software system dagobah , which includes figenix libraries which provide pipeline analysis. to evaluate the genomic similarity between studied genomes, we determined two parameters, digital ddh (dddh), which exhibits a high correlation […]

PMCID: 5552949
PMID: 28326685
DOI: 10.1002/mbo3.458

[…] was done to determine the predicted genes functional classes’ distribution according to the clusters of orthologous groups of proteins. the multi‐agent software system dagobah, which includes figenix libraries for provide pipeline analysis and phylopattern for tree manipulation, was used to perform the annotation and comparison processes (gouret et al., ). genome‐to‐genome distance […]


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FIGENIX institution(s)
Phylogenomics Laboratory. EA 3781 EGEE (Evolution, Genome, Environment), Université de Provence, Marseille, France ; AFMB-UMR 6098- CNRS - U1 - U2 Glycogenomics and Biomedical Structural Biology, Marseille, France

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