Simultaneous prediction of transcription factor binding sites in a group of prokaryotic genomes
摘要：
p pBackground/p pOur 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 itde novo /itgenome-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./p pResults/p pHere, 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 itγ/it-proteobacterial genomes including itE. coli /itK12, a group of firmicutes genomes including itB. subtilis /itand a group of cyanobacterial genomes using the same parameter settings, eGLECLUBS predicts more than 82% of known TFBSs in extracted inter-operonic sequences in both itE. coli /itK12 and itB. subtilis/it. Because each genome in a group is equally treated, it is highly likely that similar prediction accuracy has been achieved for each genome in the group./p pConclusions/p pWe have developed a new algorithm for genome-wide itde novo /itprediction of TFBSs in a group of related prokaryotic genomes. The algorithm has achieved the same level of accuracy and robustness as its predecessor GLECLUBS, but can work on dozens of genomes at the same time./p
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关键词：
Bacteria Escherichia coli Transcription Factors Chromosome Mapping Sequence Analysis, DNA Phylogeny Genome, Bacterial Binding Sites Genome-Wide Association Study Algorithms
DOI：
10.1186/1471-2105-11-397
被引量：
年份：
2010
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