Supported Applications

ORF-RATER

  • Description

    (Open Reading Frame - Regression Algorithm for Translational Evaluation of Ribosome-protected footprints) comprises a series of scripts for coding sequence annotation based on ribosome profiling data.

  • Usage Notes

    ORF-RATER comprises several python scripts.

    These scripts can be called as executables from within the BioGrids environment.

    find_orfs_and_types.py

    make_orf_bed.py

    make_tfams.py

    prune_transcripts.py

    psite_trimmed.py

    quantify_orfs.py

    regress_orfs.py

    rate_regression_output.py

    In addition, the version of python included with ORF-RATER can be called with the alias: python.orfrater

  • Installation

    Use the following command to install this title with the CLI client: $ biogrids-cli install orfrater Copy to clipboard
  • Primary Citation*

    A. P. Fields, E. H. Rodriguez, M. Jovanovic, N. Stern-Ginossar, B. J. Haas, P. Mertins, R. Raychowdhury, N. Hacohen, S. A. Carr, N. T. Ingolia, A. Regev, and J. S. Weissman. 2015. A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation. Mol Cell. 60(5): 816-827.


    • *Full citation information available through

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