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Imogene specifications

Information


Unique identifier OMICS_12898
Name Imogene
Interface Web user interface
Restrictions to use None
Input data A coordinate file, a file containing a list of motif definitions.
Output format .txt
Programming languages C++, Python
License GNU General Public License version 3.0
Computer skills Basic
Version 1.0-253
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Vincent Hakim

Information


Unique identifier OMICS_12898
Name Imogene
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A coordinate file, a file containing a list of motif definitions.
Output format .txt
Operating system Unix/Linux
Programming languages C++, Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0-257
Stability Stable
Requirements
GNU Scientific, Corebio, weblogo, argparse
Maintained Yes

Download


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Versioning


No version available

Documentation


Maintainer


  • person_outline Vincent Hakim

Publication for Imogene

Imogene citations

 (2)
library_books

MyoD reprogramming requires Six1 and Six4 homeoproteins: genome wide cis regulatory module analysis

2016
Nucleic Acids Res
PMCID: 5062961
PMID: 27302134
DOI: 10.1093/nar/gkw512

[…] itive synergistic CRMs, and whether their expression was impaired in SixdKO MEFs. In order to do this we first bioinformatically explored the TF motif content of the 14 synergistic CRMs. We used both Imogene, a de novo motif generator which relies on phylogeny and inter-species motif conservation (), and the available set of PWMs from Transfac and Jaspar databases (see Materials and Methods). The […]

library_books

Six Homeoproteins and a linc RNA at the Fast MYH Locus Lock Fast Myofiber Terminal Phenotype

2014
PLoS Genet
PMCID: 4031048
PMID: 24852826
DOI: 10.1371/journal.pgen.1004386

[…] ly tested by Electrophoretic Mobility Shift Assay on the basis of their proximity to the MEF3 Myogenin consensus GAAACCTGA . The PWM (shown in and ) was generated by running the de novo motif finder Imogene on small DNA fragments (see ) that contained these binding sites. Imogene used phylogeny to enrich mouse set of DNA fragments with orthologs in 11 other mammalian sequenced genomes and to pro […]


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Imogene institution(s)
Developmental and Stem Cell Biology Department, Institut Pasteur, Paris, France; CNRS, URA2578, Paris, France; Laboratoire de Physique Statistique, CNRS, Ecole Normale Supérieure, Université P et M Curie, Université Paris-Diderot, France
Imogene funding source(s)
Centre National de la Recherche Scientifique; Ecole Normale Supérieure; Institut Pasteur; Agence Nationale pour la Recherche [ANR-08-BLAN-0235]

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