Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat

Genome Res. 2004 Apr;14(4):700-7. doi: 10.1101/gr.1976004.

Abstract

We generalize the computation of the Regulatory Potential (RP) score from two-way alignments of human and mouse to three-way alignments of human, mouse, and rat. This requires overcoming technical challenges that arise because the complexity of the models underlying the score increases exponentially with the number of species. Despite the close evolutionary proximity of rat to mouse, we find that adding the rat sequence increases our ability to predict genomic sites that regulate gene transcription. A variant of the RP scoring scheme that accounts for local variation in neutral mutational patterns further improves our predictions.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Actins / genetics
  • Animals
  • CCAAT-Enhancer-Binding Protein-alpha / genetics
  • Computational Biology / methods
  • Computational Biology / statistics & numerical data
  • DNA / genetics
  • Enhancer Elements, Genetic / genetics
  • Evolution, Molecular
  • Genetic Variation / genetics
  • Genome*
  • Genome, Human*
  • Humans
  • Mice
  • Rats
  • Regulatory Sequences, Nucleic Acid / genetics*
  • Sequence Alignment / methods*
  • Sequence Alignment / statistics & numerical data

Substances

  • Actins
  • CCAAT-Enhancer-Binding Protein-alpha
  • DNA