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Related Concept Videos

Genome Annotation and Assembly03:36

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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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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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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
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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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DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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Navigating Eukaryotic Genome Annotation Pipelines: A Route Map to Using BRAKER, Galba, and TSEBRA.

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Summary

Accurate eukaryotic genome annotation is crucial for gene function studies. BRAKER and Galba are automated pipelines that improve gene structure prediction using different evidence sources, offering practical guidelines for their use.

Keywords:
AUGUSTUSBRAKERBUSCOCompleasmGalbaGene predictionGeneMark-ETPGenome annotationIso-SeqMiniprotPipelineProtein-coding genesRNA-SeqSpliced alignmentTSEBRA

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Accurate annotation of protein-coding genes is essential for eukaryotic genome analysis and understanding gene function.
  • Automated pipelines simplify the complex task of genome annotation.
  • Existing tools face challenges with varying genome sizes and data availability.

Purpose of the Study:

  • To provide practical guidelines for using two automated genome annotation pipelines: BRAKER and Galba.
  • To compare the performance and methodologies of BRAKER and Galba for eukaryotic genome annotation.
  • To highlight their utility, particularly for insect genomes.

Main Methods:

  • BRAKER integrates GeneMark-ETP and AUGUSTUS gene finders, using TSEBRA for high sensitivity and precision.
  • BRAKER utilizes transcript expression data and protein databases for annotation.
  • Galba uses protein-to-genome spliced alignments (miniprot) to generate training data for AUGUSTUS, excelling with protein evidence alone.

Main Results:

  • BRAKER achieves high accuracy with both transcript and protein evidence, adaptable to various genome sizes.
  • Galba demonstrates superior accuracy for large genomes when only protein sequences are available.
  • Both pipelines offer robust solutions for automated genome annotation.

Conclusions:

  • BRAKER and Galba are effective, automated pipelines for eukaryotic genome annotation.
  • The choice between BRAKER and Galba depends on data availability and genome characteristics.
  • These pipelines provide valuable tools for genomic research, especially in fields like insect genomics.