Biochemistry Publications


BIPAD: A Web Server for Modeling Bipartite Sequence Elements

Document Type


Publication Date



BMC Bioinformatics






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 [1], 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.


Published in: BMC Bioinformatics 2006, 7:76doi:10.1186/1471-2105-7-76. The electronic version of this article is the complete one and can be found online at: Dr. Peter K. Rogan is currently a faculty member at the University of Western Ontario.