Phylogenomic resources at the UCSC Genome Browser.

Kate Rosenbloom, James Taylor, Stephen Wade Schaeffer, Jim Kent, David Haussler, Webb Miller

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)133-144
Number of pages12
JournalMethods in molecular biology (Clifton, N.J.)
Volume422
StatePublished - Jan 1 2008

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Genome
Vertebrates
Sequence Alignment
Human Genome
Insect Genome

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

Cite this

Rosenbloom, K., Taylor, J., Schaeffer, S. W., Kent, J., Haussler, D., & Miller, W. (2008). Phylogenomic resources at the UCSC Genome Browser. Methods in molecular biology (Clifton, N.J.), 422, 133-144.
Rosenbloom, Kate ; Taylor, James ; Schaeffer, Stephen Wade ; Kent, Jim ; Haussler, David ; Miller, Webb. / Phylogenomic resources at the UCSC Genome Browser. In: Methods in molecular biology (Clifton, N.J.). 2008 ; Vol. 422. pp. 133-144.
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Rosenbloom, K, Taylor, J, Schaeffer, SW, Kent, J, Haussler, D & Miller, W 2008, 'Phylogenomic resources at the UCSC Genome Browser.', Methods in molecular biology (Clifton, N.J.), vol. 422, pp. 133-144.

Phylogenomic resources at the UCSC Genome Browser. / Rosenbloom, Kate; Taylor, James; Schaeffer, Stephen Wade; Kent, Jim; Haussler, David; Miller, Webb.

In: Methods in molecular biology (Clifton, N.J.), Vol. 422, 01.01.2008, p. 133-144.

Research output: Contribution to journalArticle

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Rosenbloom K, Taylor J, Schaeffer SW, Kent J, Haussler D, Miller W. Phylogenomic resources at the UCSC Genome Browser. Methods in molecular biology (Clifton, N.J.). 2008 Jan 1;422:133-144.