BIPAD: a web server for modeling bipartite sequence elements

BMC Bioinformatics
Chengpeng Bi, Peter K Rogan

Abstract

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. 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. 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.

References

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Sep 25, 2004·Nucleic Acids Research·Chengpeng Bi, Peter K Rogan

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Citations

Apr 13, 2013·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Onuma ChumsakulShu Ishikawa
Jul 9, 2008·Current Opinion in Lipidology·E Shyong Tai, Jose M Ordovas
Sep 2, 2009·Microbiology and Molecular Biology Reviews : MMBR·Sacha A F T van HijumOscar P Kuipers
Aug 12, 2014·Applied Microbiology and Biotechnology·Cláudia M VicenteJesús F Aparicio
Feb 27, 2015·Applied Microbiology and Biotechnology·Cláudia M VicenteJesús F Aparicio
Jan 25, 2020·Nature Communications·Timothy T HardenJeff Gelles
Dec 14, 2007·Molecular Pharmaceutics·Chengpeng BiCarrie A Vyhlidal

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Methods Mentioned

BETA
immunoprecipitation
ChIP-chip

Software Mentioned

Bipad
Gibbs Sampler
BioProspector
seqlogo
GLAM
CONSENSUS

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