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Related Concept Videos

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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Genomics02:02

Genomics

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Genomic Imprinting and Inheritance02:30

Genomic Imprinting and Inheritance

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Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
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Protein Complex Assembly02:41

Protein Complex Assembly

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Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
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Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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Related Experiment Video

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Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products
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AGILE: an assembled genome mining pipeline.

Graham M Hughes1, Emma C Teeling1

  • 1School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland.

Bioinformatics (Oxford, England)
|September 6, 2018
PubMed
Summary

This study introduces AGILE, a Perl pipeline for mining coding sequences in fragmented genome assemblies. AGILE overcomes limitations of traditional tools, enabling non-specialists to access valuable genomic data.

Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Traditional genome annotation tools struggle with poor quality or fragmented genome assemblies.
  • This limitation restricts data accessibility to specialists in genome assembly and annotation.

Purpose of the Study:

  • To present an Assembled-Genome mIning pipeLinE (AGILE) to overcome limitations in annotating fragmented genomes.
  • To enable non-specialists to mine and annotate coding sequences from challenging genome assemblies.

Main Methods:

  • AGILE is a Perl-based pipeline combining bioinformatics tools and custom steps.
  • It uses user-specified query genes from related species to identify and annotate coding sequences.
  • The methodology is designed to handle highly fragmented genomes.

Main Results:

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  • AGILE successfully mines and annotates coding sequences missed by standard annotation packages.
  • The pipeline effectively addresses limitations imposed by poor quality genome assemblies.

Conclusions:

  • AGILE provides a generalized solution applicable to any genome assembly, not limited to mammalian genomes.
  • It empowers non-specialists to gather gene sequences for downstream analyses from challenging genomic data.