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Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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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.
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Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
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Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
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GENCODE: reference annotation for the human and mouse genomes in 2023.

Adam Frankish1, Sílvia Carbonell-Sala2, Mark Diekhans3

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|November 24, 2022
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Summary
This summary is machine-generated.

GENCODE provides high-quality gene and transcript annotation for human and mouse genomes, validated by experimental data. This update details advancements in tools, data, and collaborations for improved genome annotation and functional determination.

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Area of Science:

  • Genomics
  • Transcriptomics
  • Bioinformatics

Background:

  • GENCODE provides comprehensive gene and transcript annotation for human and mouse genomes.
  • Annotation is crucial for genome biology and clinical genomics applications.
  • The GENCODE consortium integrates experimental data and bioinformatic analyses.

Purpose of the Study:

  • To present an update on GENCODE annotation for human and mouse genes.
  • To highlight advancements in annotation tools, data, and analytical methods.
  • To report on key collaborations and their impact on annotation quality and scope.

Main Methods:

  • Generation of targeted experimental data.
  • Development and application of bioinformatic tools for transcript identification and annotation.
  • Integration of external data and collaborative efforts with RefSeq and UniProt.
  • Analysis of long transcriptomic data for model building (LRGASP).

Main Results:

  • Identification and annotation of non-canonical open reading frames (ORFs).
  • Increased convergence in human and mouse protein-coding gene annotation through collaborations.
  • Expansion of GENCODE annotation across the human pan-genome.
  • Development of new tools for regulatory feature annotation.

Conclusions:

  • GENCODE annotation is a continuously improving reference standard for genomic research.
  • Collaborations and technological advancements enhance the accuracy and breadth of gene annotation.
  • The updated GENCODE release supports diverse applications in basic and clinical genomics.