DeepShape

DeepShape is a computational tool that utilizes deep learning to analyze ribosome profiling (Ribo-seq) data. It addresses the challenge of assigning multiple-mapped reads to similar isoforms by estimating ribosome abundance and generating ribosome profiles at the transcript level without relying on RNA-seq data.

DeepShape introduces the "Codon Residence Index" to analyze ribosome distributions and investigate the relative speed of ribosomes on codons compared to their synonymous codons.

Topic

Cell biology;Gene expression;Protein expression;RNA-Seq;Gene transcripts

Detail

  • Operation: Multiple sequence alignment;RNA-Seq quantification;Expression analysis

  • Software interface: Command-line interface

  • Language: Python

  • License: Not stated

  • Cost: Free of charge

  • Version name: -

  • Credit: National Natural Science Foundation of China, Beijing National Research Center for Information Science and Technology, China’s Youth 1000-Talent Program, and Beijing Advanced Innovation Center for Structural Biology.

  • Input: -

  • Output: -

  • Contact: Jianyang Zeng zengjy321@tsinghua.edu.cn ,Ting Chen tingchen@tsinghua.edu.cn

  • Collection: -

  • Maturity: -

Publications

  • DeepShape: estimating isoform-level ribosome abundance and distribution with Ribo-seq data.
  • Cui H, et al. DeepShape: estimating isoform-level ribosome abundance and distribution with Ribo-seq data. DeepShape: estimating isoform-level ribosome abundance and distribution with Ribo-seq data. 2019; 20:678. doi: 10.1186/s12859-019-3244-0
  • https://doi.org/10.1186/S12859-019-3244-0
  • PMID: 31861979
  • PMC: PMC6923924

Download and documentation

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