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Related Concept Videos

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 DNA in Eukaryotes00:58

Genomic DNA in Eukaryotes

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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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Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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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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Genome-wide Snapshot of Chromatin Regulators and States in Xenopus Embryos by ChIP-Seq
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Xenbase: a genomic, epigenomic and transcriptomic model organism database.

Kamran Karimi1, Joshua D Fortriede2, Vaneet S Lotay1

  • 1Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada.

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Xenbase is an updated online resource for Xenopus researchers, offering new genomes, RNA-Seq visualization, and improved data integration. It supports biomedical scientists using these model organisms.

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Area of Science:

  • Comparative genomics
  • Bioinformatics
  • Developmental biology

Background:

  • Xenopus laevis and Xenopus tropicalis are crucial model organisms in biological research.
  • Access to curated data and bioinformatic tools is essential for Xenopus research.
  • High-throughput sequencing technologies have generated vast amounts of data for these species.

Purpose of the Study:

  • To update and enhance the Xenbase online resource for Xenopus researchers.
  • To incorporate new data types and functionalities reflecting advances in sequencing technologies.
  • To improve data accessibility and integration for biomedical scientists.

Main Methods:

  • Aggregation of data from external resources.
  • In-house curation of scientific literature.
  • Bioinformatic analyses and development of new tools.
  • Integration of high-throughput sequencing data, including RNA-Seq and ChIP-Seq.

Main Results:

  • Introduction of new chromosome-scale genome assemblies for Xenopus laevis and Xenopus tropicalis.
  • Enhanced genome annotations and segmentation capabilities.
  • Dynamic and interactive visualization tools for RNA-Seq data.
  • Updated ChIP-Seq mapping, Gene Ontology (GO) terms, and protein interaction data.
  • Improved connectivity with other biomedical and bioinformatic resources.

Conclusions:

  • Xenbase provides a comprehensive and up-to-date resource for the Xenopus research community.
  • The enhancements facilitate the analysis of high-throughput sequencing data.
  • Xenbase supports biomedical research by providing integrated data for Xenopus model systems.