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Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
Proteomics01:33

Proteomics

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.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
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Ribosome Profiling

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.
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RNA-seq03:21

RNA-seq

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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Updated: Jun 30, 2026

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

Subproteomic tools to increase genome annotation complexity.

Candong Wei1, Junping Peng, Zhaohui Xiong

  • 1State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of Medical Sciences, Beijing, P. R. China.

Proteomics
|September 25, 2008
PubMed
Summary
This summary is machine-generated.

Researchers developed a new method combining shotgun proteomics and oligonucleotide arrays to identify short protein-coding genes. This approach successfully validated numerous genes and discovered novel ones in Shigella flexneri, improving genome annotation.

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Area of Science:

  • Genomics
  • Proteomics
  • Microbiology

Background:

  • Accurate annotation of short protein-coding genes is difficult.
  • Previously overlooked short genes pose challenges in genome analysis.

Purpose of the Study:

  • To develop an integrated strategy for characterizing short protein-coding genes.
  • To improve the comprehensive and precise annotation of prokaryotic genomes.

Main Methods:

  • Integration of shotgun proteomics and oligonucleotide array analysis.
  • Application of the strategy to Shigella flexneri as a model organism.

Main Results:

  • Validation of 163 annotated open reading frames (ORFs) and 51 hypothetical or putative transcripts at the protein level.
  • Discovery of four novel short ORFs.
  • Demonstration of the method's efficacy in identifying previously uncharacterized genes.

Conclusions:

  • The proposed strategy significantly enhances genome-wide annotation accuracy.
  • This approach deepens the understanding of prokaryotic genome structure and gene content.