SpringerProtocols: Abstract: 9. Phylogenomic Resources at the UCSC Genome Browser

9. Phylogenomic Resources at the UCSC Genome Browser

By: Kate Rosenbloom³, James Taylor⁴, Stephen Schaeffer⁵, Jim Kent³, David Haussler⁶, Webb Miller⁴

Abstract

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The UC Santa Cruz Genome Browser provides a number of resources that can be used for phylogenomic studies, including (1) whole-genome sequence data from a number of vertebrate species, (2) pairwise alignments of the human genome sequence to a number of other vertebrate genome, (3) a simultaneous alignment of 17 vertebrate genomes (most of them incompletely sequenced) that covers all of the human sequence, (4) several independent sets of multiple alignments covering 1% of the human genome (ENCODE regions), (5) extensive sequence annotation for interpreting those sequences and alignments, and (6) sequence, alignments, and annotations from certain other species, including an alignment of nine insect genomes. We illustrate the use of these resources in the context of assigning rare genomic changes to the branch of the phylogenetic tree where they appear to have occurred, or of looking for evidence supporting a particular possible tree topology. Sample source code for performing such studies is available.

Affiliation(s): (3) Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA
(4) Center for Comparative Genomics and Bioinformatics, Penn State, University Park, PA
(5) Department of Biology, Penn State, University Park, PA
(6) Howard Hughes Medical Institute, University of California, Santa Cruz, CA

Book Title: Phylogenomics

Series: Methods in Molecular Biology | Volume: 422 | Pub. Date: Dec-16-2007 | Page Range: 133-144 | DOI: 10.1007/978-1-59745-581-7_9

Subject: Cell Biology

Key Words: Evolutionary event - phylogenetic tree - interspersed repeat - chromosomal break

References

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