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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
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Ribosomes01:27

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Ribosomes translate genetic information encoded by messenger RNA (mRNA) into proteins. Both prokaryotic and eukaryotic cells have ribosomes. Cells that synthesize large quantities of protein—such as secretory cells in the human pancreas—can contain millions of ribosomes.
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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Modification of secretory and transmembrane proteins entering the rough ER begins in the ER lumen. These modifications aid in protein folding and stabilize the acquired tertiary structure. Protein modifications in the rough ER co-occur at different stages of protein folding.
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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
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De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
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RiboChat: a chat-style web interface for analysis and annotation of ribosome profiling data.

Mingzhe Xie1, Ludong Yang1, Gennong Chen1

  • 1State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China.

Briefings in Bioinformatics
|January 19, 2022
PubMed
Summary

Researchers can now easily analyze ribosome profiling (Ribo-seq) data using RiboChat, a novel web platform. This tool simplifies complex bioinformatics, making translation information accessible to all scientists.

Keywords:
chat interfacedata analysisinteractive miningribosome profilingvisualization

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Ribosome profiling (Ribo-seq) generates vast amounts of data, posing significant computational and analytical challenges.
  • Limited bioinformatics expertise creates a barrier for researchers analyzing Ribo-seq data to understand translation.
  • There is a need for simplified, accessible tools for Ribo-seq data analysis and information extraction.

Purpose of the Study:

  • To introduce RiboChat, an interactive web platform designed for direct analysis and annotation of Ribo-seq data.
  • To overcome the informatics challenges associated with Ribo-seq data processing.
  • To enable researchers with limited bioinformatics experience to decode translation information.

Main Methods:

  • Development of a user-friendly web interface integrated with a backend cloud-computing service.
  • Implementation of an object-text detection module to identify keywords from user queries.
  • A scoring system to match user questions with appropriate analytical modules for execution.

Main Results:

  • RiboChat provides a conversational interface for Ribo-seq data analysis.
  • The platform automates the selection and execution of relevant analytical modules based on user input.
  • Successful integration of data uploading and parameter configuration for analysis.

Conclusions:

  • RiboChat represents a significant advancement in next-generation data analytics for Ribo-seq.
  • The platform lowers the barrier for researchers to analyze and interpret translation information from Ribo-seq data.
  • RiboChat empowers the broader research community to conveniently decipher complex biological data.