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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.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>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.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-7-76","type":"journal-article","created":{"date-parts":[[2006,2,24]],"date-time":"2006-02-24T07:30:36Z","timestamp":1140766236000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["BIPAD: A web server for modeling bipartite sequence elements"],"prefix":"10.1186","volume":"7","author":[{"given":"Chengpeng","family":"Bi","sequence":"first","affiliation":[]},{"given":"Peter K","family":"Rogan","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2006,2,17]]},"reference":[{"key":"815_CR1","volume-title":"Bipad","author":"CP Bi","year":"2004","unstructured":"Bi CP, Rogan PK: Bipad.2004. 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