Simultaneous prediction of transcription factor binding sites in a group of prokaryotic genomes

Background: Our current understanding of transcription factor binding sites (TFBSs) in sequenced prokaryotic genomes is very limited due to the lack of an accurate and efficient computational method for the prediction of TFBSs at a genome scale. In an attempt to change this situation, we have recently developed a comparative genomics based algorithm called GLECLUBS for de novo genome-wide prediction of TFBSs in a target genome. Although GLECLUBS has achieved rather high prediction accuracy of TFBSs in a target genome, it is still not efficient enough to be applied to all the sequenced prokaryotic genomes. Results: Here, we designed a new algorithm based on GLECLUBS called extended GLECLUBS (eGLECLUBS) for simultaneous prediction of TFBSs in a group of related prokaryotic genomes. When tested on a group of gproteobacterial genomes including E. coli K12, a group of firmicutes genomes including B. subtilis and a group of cyanobacterial genomes using the same parameter settings, eGLECLUBS...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Shaoqiang Zhang, Shan Li, Phuc T. Pham, Zhengchang Su
• Keywords: BMCBI 2010, Genome, Prediction, Prokaryotic Genomes