Genomics Inform.  2011 Dec;9(4):194-196.

PromoterWizard: An Integrated Promoter Prediction Program Using Hybrid Methods

• Park K
• Kim KB

Abstract

Promoter prediction is a very important problem and is closely related to the main problems of bioinformatics such as the construction of gene regulatory networks and gene function annotation. In this context, we developed an integrated promoter prediction program using hybrid methods, PromoterWizard, which can be employed to detect the core promoter region and the transcription start site (TSS) in vertebrate genomic DNA sequences, an issue of obvious importance for genome annotation efforts. PromoterWizard consists of three main modules and two auxiliary modules. The three main modules include CDRM (Composite Dependency Reflecting Model) module, SVM (Support Vector Machine) module, and ICM (Interpolated Context Model) module. The two auxiliary modules are CpG Island Detector and GCPlot that may contribute to improving the predictive accuracy of the three main modules and facilitating human curator to decide on the final annotation.

Keyword

regulatory networks; TSS; CDRM; SVM; CpG Island detector; GCPlot

MeSH Terms

Base Sequence
Chimera
Computational Biology
CpG Islands
Dependency (Psychology)
Gene Regulatory Networks
Genome
Humans
Promoter Regions, Genetic
Transcription Initiation Site
Vertebrates