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Comparative Genomic Analysis Using the UCSC Genome Browser

  • Donna Karolchik
  • Gill Bejerano
  • Angie S. Hinrichs
  • Robert M. Kuhn
  • Webb Miller
  • Kate R. Rosenbloom
  • Ann S. Zweig
  • David Haussler
  • W. James Kent
Part of the Methods in Molecular Biology™ book series (MIMB, volume 395)

Summary

Comparative analysis of DNA sequence from multiple species can provide insights into the function and evolutionary processes that shape genomes. The University of California Santa Cruz (UCSC) Genome Bioinformatics group has developed several tools and methodologies in its study of comparative genomics, many of which have been incorporated into the UCSC Genome Browser (http://genome.ucsc.edu), an easy-to-use online tool for browsing genomic data and aligned annotation “tracks” in a single window. The comparative genomics annotations in the browser include pairwise alignments, which aid in the identification of orthologous regions between species, and conservation tracks that show measures of evolutionary conservation among sets of multiply aligned species, highlighting regions of the genome that may be functionally important.A related tool, the UCSC Table Browser, provides a simple interface for querying, analyzing,and downloading the data underlying the Genome Browser annotation tracks. Here, we describe a procedure for examining a genomic region of interest in the Genome Browser, analyzing characteristics of the region, filtering the data, and downloading data sets for further study.

Key Words

Comparative genomics UCSC Genome Browser UCSC Table Browser cross-species alignments evolutionary conservation orthology 

Notes

Acknowledgments

The UCSC Genome Browser project is funded by grants from the National Human Genome Research Institute (NHGRI), the Howard Hughes Medical Institute (HHMI), and the National Cancer Institute (NCI). We would like to acknowledge the excellent work of the Genome Browser technical staff who maintain and enhance the Genome Browser database and software, the many collaborators who have contributed annotation data to the project, and our loyal users for their feedback and support.

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Copyright information

© Humana Press Inc. 2007

Authors and Affiliations

  • Donna Karolchik
    • 1
  • Gill Bejerano
    • 2
  • Angie S. Hinrichs
    • 3
  • Robert M. Kuhn
    • 4
  • Webb Miller
    • 5
  • Kate R. Rosenbloom
    • 6
  • Ann S. Zweig
    • 7
  • David Haussler
    • 8
  • W. James Kent
    • 9
  1. 1.UCSC Genome Bioinformatics Group, Center for Biomolecular Science and EngineeringUniversity of CaliforniaSanta Cruz
  2. 2.UCSC Genome Bioinformatics Group, Center for Biomolecular Science, and EngineeringUniversity of CaliforniaSanta Cruz
  3. 3.UCSC Genome Bioinformatics Group, Center for Biomolecular Science and EngineeringUniversity of CaliforniaSanta Cruz
  4. 4.UCSC Genome Bioinformatics Group, Center for Biomolecular Science and EngineeringUniversity of CaliforniaSanta Cruz
  5. 5.CCGBPenn State UniversityPennsylvania
  6. 6.UCSC Genome Bioinformatics Group, Center for Biomolecular Science and EngineeringUniversity of CaliforniaSanta Cruz
  7. 7.UCSC Genome Bioinformatics Group, Center for Biomolecular Science and EngineeringUniversity of CaliforniaSanta Cruz
  8. 8.UCSC Genome Bioinformatics Group, Center for Biomolecular Science and EngineeringHoward Hughes Medical Institute, University of CaliforniaSanta Cruz
  9. 9.UCSC Genome Bioinformatics Group, Center for Biomolecular Science and EngineeringUniversity of CaliforniaSanta Cruz

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