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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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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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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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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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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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Bioinformatics for Analysis of Poxvirus Genomes.

Shin-Lin Tu1, Chris Upton2

  • 1Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.

Methods in Molecular Biology (Clifton, N.J.)
|June 27, 2019
PubMed
Summary

Recent advances in genome sequencing provide valuable data for virologists. This work introduces bioinformatics tools to help researchers analyze poxvirus genomes, overcoming common data management and analysis challenges.

Keywords:
BBBBLASTBioinformaticsDotplotGenomicsJDotterMSAMultiple sequence alignmentPoxvirusSmallpoxVGOVOCsVaccinia virus

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Virology

Background:

  • Technological advancements in molecular biology, particularly genome sequencing, have generated vast amounts of data.
  • The analysis of this data is crucial for virologists, especially in the study of poxviruses.
  • Existing public databases can be cumbersome for managing and analyzing large-scale viral genomic data.

Purpose of the Study:

  • To address the challenges faced by bench virologists in accessing, analyzing, and interpreting genomics data.
  • To introduce user-friendly software solutions for bioinformatics-based experiments.
  • To focus on the comparison and analysis of poxvirus genomes.

Main Methods:

  • Description of software to overcome common bioinformatics hurdles.
  • Highlighting the Viral Orthologous Clusters (VOC) database system.
  • Integration of tools for management and analysis of complete viral genomes.

Main Results:

  • Identification of common obstacles in genomics data handling for researchers.
  • Presentation of solutions through intuitive software.
  • Demonstration of efficient data management and analysis for viral genomes.

Conclusions:

  • User-friendly bioinformatics software is critical for bench virologists.
  • The Viral Orthologous Clusters system offers an effective solution for poxvirus genome analysis.
  • Streamlined data management and analysis facilitate virological research.