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BIPAD: a web server for modeling bipartite sequence elements.

Chengpeng Bi1, Peter K Rogan

  • 1Laboratory of Human Molecular Genetics, Children's Mercy Hospital & Clinics, Kansas City, MO 64108, USA. cbi@cmh.edu

BMC Bioinformatics
|March 1, 2006
PubMed
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The Bipad Server predicts DNA binding sites by identifying sequence elements in unaligned DNA. It uses position weight matrices and gap distributions to model cooperative protein binding, aiding in the discovery of regulatory motifs.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Dimeric protein complexes often bind cooperatively to bipartite nucleic acid sequences.
  • These sequences feature conserved half-sites separated by variable distances.

Purpose of the Study:

  • To develop a web server, Bipad Server, for predicting sequence elements within unaligned DNA sequences.
  • To provide a tool for identifying potential binding sites for dimeric proteins.

Main Methods:

  • The Bipad program employs multiple local alignment via entropy minimization and cyclic refinement.
  • A stochastic greedy search strategy is used for model refinement.
  • Models are refined by maximizing incremental information content for varying half-site and gap lengths.

Related Experiment Videos

Main Results:

  • The Bipad Server can generate bipartite models (position weight matrices with gap distributions) or single PWMs for contiguous motifs.
  • It identifies binding site motifs and generates positional weight matrices.
  • Graphical representations include sequence logos and gap distribution histograms.

Conclusions:

  • The Bipad Server is a valuable web service for discovering DNA binding site motifs.
  • Its performance was validated by modeling bipartite elements for various DNA-binding proteins.