PromSearch: A Hybrid Approach to Human Core-Promoter Prediction

This paper presents an effective core-promoter prediction system on human DNA sequence. The system, named PromSearch, employs a hybrid approach which combines search-by-content method and search-by-signal method. Global statistics of promoter-specific contents are included to represent new significant information underlying the proximal and downstream region around transcription start site (TSS) of DNA sequence. Local signal features such as TATA box and CAAT box are encoded by the position weight matrix (PWM) method. In the experiment for the sequence set from the review by J.W.Fickett, PromSeach shows 47% positive predictive value which surpasses most of previously systems. On large genomic sequences, it shows reduced false positive rate while preserving true positive rate.