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Quantifies isoform-level ribosome profiles. Ribomap is a conceptual framework and software that produces accurate isoform specific ribosome profiles by accounting for multi-mapping sequence reads using RNA-seq estimates of isoform abundance. The software works in three stages: (i) Transcript abundance estimation, (ii) Mapping ribo-seq reads to the reference transcriptome and (iii) Ribosome profile estimation. It can serve as a useful first step for downstream analysis of translational regulation from ribo-seq data.
Predicts ribosome footprint profile shapes from transcript sequences. Riboshape is a suite of algorithms. It applies kernel smoothing to codon sequences to build predictive features, and uses these features to builds a sparse regression model to predict the ribosome footprint profile shapes. It also proposes a wide range of applications, including inferring isoform-specific ribosome footprints, designing transcripts with fast translation speeds and discovering unknown modulation during translation.
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