Format

Send to

Choose Destination
BMC Bioinformatics. 2006 Feb 17;7:76.

BIPAD: a web server for modeling bipartite sequence elements.

Author information

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

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.

PMID:
16503993
PMCID:
PMC1388241
DOI:
10.1186/1471-2105-7-76
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for BioMed Central Icon for PubMed Central
Loading ...
Support Center