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Associated diseases

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GenRGenS specifications

Information


Unique identifier OMICS_20902
Name GenRGenS
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.1
Stability Stable
Source code URL https://www.lri.fr/genrgens/distribution//GenRGenS2.1-src.zip
Maintained Yes

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Documentation


Maintainer


  • person_outline Alain Denise <>

Additional information


https://www.lri.fr/genrgens/manual/GRGs-manual-html/index.html https://www.lri.fr/genrgens/index.php?idpage=1

Publication for GenRGenS

GenRGenS in publications

 (4)
PMCID: 3821693
PMID: 24228136
DOI: 10.4161/cib.24951

[…] studies of four specific crop plants (tobacco, potato, pepper and cowpea) for which there were only incomplete viral genomes available. finally, we performed a statistical analysis on the results. genrgens software was utilized to randomly generate genomics sequences. we created randomized versions of every single plant virus genome in the dpv database. the settings used were the markov model, […]

PMCID: 3125259
PMID: 21738721
DOI: 10.1371/journal.pone.0021590

[…] random sequences produced by randomly shuffling codons within each coding sequence deprived of its first and last nucleotide triplets., randnuc and randcod sequences were generated by the software genrgens . shufcod sequences were generated using the fisher-yates algorithm . for simulation procedures, nucleotide and codon frequencies from native cdss were computed without considering […]

PMCID: 2996987
PMID: 20828396
DOI: 10.1186/1471-2164-11-491

[…] of gene lengths in the target genome were generated using second-order and fifth-order three-periodic markov models trained on the set of coding sequences, as implemented in the markov package of genrgens []. the expected frequencies of osc occurrences in the simulated sequences were then compared to the frequencies observed in the actual sequences using the one-sample t-test, with correction […]

PMCID: 1282332
PMID: 16292353
DOI: 10.1371/journal.pcbi.0010056

[…] genes that have evolved under similar conditions can be described by a distinct model. while simple models for artificial genome construction based on nucleotide or hexamer statistics (e.g., genrgens [http://www.lri.fr/~denise/genrgens/]) are suitable for examination of regulatory interactions or performance of artificial life simulations [,], more sophisticated models are required […]


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GenRGenS institution(s)
LRI, UMR CNRS 8623, Université Paris-Sud 11, Orsay, France; IGM, UMR CNRS 8621, Université Paris-Sud 11, Orsay, France
GenRGenS funding source(s)
Partially supported by the French IMPG and ‘ACI IMPBio’ programs, and the CNRS Specific Action ‘Modélisation et Algorithmique des Structures d’ARN’.

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