SCS: Signal, Context, and Structure Features for Genome-Wide Human Promoter Recognition

This paper integrates the signal, context and structure features for genome-wide promoter recognition, which is critical in many DNA sequence analysis tasks. First, CpG islands are salient biological signals associated with approximately 50% mammalian promoters associated with transcription start sites. Second, the genomic context of promoters may have biological significance, which is based on n-mers (sequences of n bases long) and their statistics estimated from training samples. Third, sequence-dependent DNA flexibility originates from DNA 3D structures, and plays an important role in guiding transcription factors to the target site in promoters. Employing decision trees, we combine above signal, context and structure features to build a hierarchical promoter recognition system called SCS. Experimental results on controlled datasets and the entire human genome demonstrate that SCS is significantly superior in terms of sensitivity and specificity as compared to other state-of-the-ar...

• Type: Journal
• Year: 2010
• Where: TCBB
• Authors: Jia Zeng, Xiaoyu Zhao, Xiao-Qin Cao, Hong Yan
• Keywords: Genome-wide Promoter Recognition, Promoter, Promoter Recognition, Software Engineering, TCBB 2010