ORFscore specifications

Information


Unique identifier OMICS_20321
Name ORFscore
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Maintainers


  • person_outline Antonio Giraldez <>
  • person_outline Ariel Bazzini <>
  • person_outline Nikolaus Rajewsky <>

Publication for ORFscore

ORFscore in publications

 (2)
PMCID: 4712605
PMID: 26764022
DOI: 10.1186/s12864-016-2384-0

[…] the software allows inspection of ribosome footprints on spliced transcripts, orfs, drug effects and several bioinformatics scores such as rr-score [], te-score [] and orfscore [] in our dataset at single nucleotide resolution., we show here that the eif4a targeting translation inhibitor dmda-pata outperforms computational scoring in classifying coding […]

PMCID: 4568590
PMID: 26364619
DOI: 10.1186/s13059-015-0742-x

[…] or cell lines, and from zebrafish, fruit fly, and c. elegans (additional file : table s8). several metrics to identify translated regions from such data have been proposed [, –]; we rely here on the orfscore method used in our previous publication [], which exploits the frame-specific bias of the 5′ positions of ribosome protected fragments to distinguish actively translated regions […]


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ORFscore institution(s)
Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA; Systems Biology of Gene Regulatory Elements, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
ORFscore funding source(s)
Supported by T32GM007499, Pew Fellows Program in Biomedical Sciences, the Helmholtz Alliance on Systems Biology (MDC Systems Biology Network) and MDC funding, the Delbrück Fellows program of the MDC, the Swiss National Science Foundation, R01GM081602-06, R01GM103789-01, R01HD074078-02, F32HD071697-02, R01GM095982, R01GM097194, the Pew Scholars Program in the Biomedical Sciences, the March of Dimes and the Yale Scholars Program.

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