OPTIMIR specifications


Unique identifier OMICS_33123
Alternative name pOlymorPhisminTegratIon for MIRna
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
pysam, biopython, bowtie2, cutadapt, samtools
Maintained Yes




No version available


  • person_outline David-Alexandre Tregouet
  • person_outline Florian Thibord

Publication for pOlymorPhisminTegratIon for MIRna

OPTIMIR citation


Invited review: overview of new traits and phenotyping strategies in dairy cattle with a focus on functional traits

PMCID: 4299537
PMID: 25387784
DOI: 10.1017/S1751731114002614

[…] MIR spectroscopy, generate spectral data that reflect many characteristics of milk. Research is currently underway to investigate the use of this data for prediction of indicator traits (RobustMilk, OptiMIR, PhenoFinlait, GplusE, etc.). The main challenge posed by these data is the lack of reference data for the detection of disease, such as mastitis. A reliable pool of ‘healthy’ and ‘sick’ anima […]

OPTIMIR institution(s)
Sorbonne Universités, Université Pierre et Marie Curie, Institut National pour la Santé et la Recherche Médicale (INSERM), Unité Mixte de Recherche en Santé (UMR_S) 1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris, France; Institute for Cardiometabolism and Nutrition (ICAN), Paris, France; Laboratory of Haematology, La Timone Hospital, Marseille, France; Institut National pour la Santé et la Recherche Médicale (INSERM), Unité Mixte de Recherche en Santé(UMR_S) 1062, Nutrition Obesity and Risk of Thrombosis, Center for CardioVascular and Nutrition research (C2VN), Aix-Marseille University, Marseille, France; Centre National de Recherche en Génomique Humaine, Direction de la Recherche Fondamentale, CEA, Evry, France; CEPH, Fondation Jean Dausset, Paris, France
OPTIMIR funding source(s)
Supported by the GENMED Laboratory of Excellence on Medical Genomics (ANR-10-LABX-0013).

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