BIPAD: a web server for modeling bipartite sequence elements

BMC Bioinformatics. 2006 Feb 17;7:76. doi: 10.1186/1471-2105-7-76.

Abstract

Background: Many dimeric protein complexes bind cooperatively to families of bipartite nucleic acid sequence elements, which consist of pairs of conserved half-site sequences separated by intervening distances that vary among individual sites.

Results: We introduce the Bipad Server, a web interface to predict sequence elements embedded within unaligned sequences. Either a bipartite model, consisting of a pair of one-block position weight matrices (PWM's) with a gap distribution, or a single PWM matrix for contiguous single block motifs may be produced. The Bipad program performs multiple local alignment by entropy minimization and cyclic refinement using a stochastic greedy search strategy. The best models are refined by maximizing incremental information contents among a set of potential models with varying half site and gap lengths.

Conclusion: The web service generates information positional weight matrices, identifies binding site motifs, graphically represents the set of discovered elements as a sequence logo, and depicts the gap distribution as a histogram. Server performance was evaluated by generating a collection of bipartite models for distinct DNA binding proteins.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Base Sequence
  • Binding Sites
  • Chromosome Mapping / methods*
  • Computer Simulation
  • DNA-Binding Proteins / genetics*
  • Internet
  • Models, Genetic
  • Molecular Sequence Data
  • Online Systems
  • Protein Binding
  • Sequence Alignment / methods*
  • Sequence Analysis, DNA / methods*
  • Sequence Homology, Nucleic Acid
  • Software*
  • Transcription Factors / genetics*

Substances

  • DNA-Binding Proteins
  • Transcription Factors