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Evolutionary Relationships through Genome Comparisons02:54

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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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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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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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Microbial genome evolution is a highly dynamic process shaped by continual gene gain and loss across species and strains. This genomic flexibility allows microorganisms to adapt rapidly to environmental pressures and interactions with other organisms. Central to understanding this diversity is the distinction between the core and pan genomes.The core genome comprises the genes shared by all sampled strains of a species, representing essential functions needed for fundamental cellular processes.
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The UCSC Genome Browser database: 2014 update.

Donna Karolchik1, Galt P Barber, Jonathan Casper

  • 1Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA.

Nucleic Acids Research
|November 26, 2013
PubMed
Summary
This summary is machine-generated.

The UCSC Genome Browser provides public access to genomic data for many species, with enhanced tools for analysis and visualization. New features include improved annotation tracks and variant analysis tools for researchers.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • The UCSC Genome Browser offers a comprehensive platform for accessing and analyzing genomic data.
  • It serves as a crucial resource for researchers studying the genomes of various organisms, particularly humans and mice.

Purpose of the Study:

  • To detail recent updates and new features of the UCSC Genome Browser.
  • To highlight improvements in data accessibility, analysis tools, and user-generated data integration.

Main Methods:

  • Web-based platform development and data integration.
  • Inclusion of new annotation tracks (e.g., conservation, variation, ENCODE data).
  • Development of new software tools for variant annotation and data visualization.

Main Results:

  • Expanded database with genomic sequences and annotations for approximately 90 organisms as of September 2013.
  • Introduction of a 60-species multiple alignment conservation track and updated UCSC Genes tracks.
  • New tools like Variant Annotation Integrator and enhanced data hub capabilities for user-provided data.

Conclusions:

  • The UCSC Genome Browser continues to evolve as a powerful, integrated resource for genomic research.
  • Recent updates enhance data analysis capabilities, particularly for genetic variation and comparative genomics.
  • Improved European accessibility through a new mirror site facilitates broader global research collaboration.