Contribution of bacterial promoter elements to transcription start site detection accuracy

Accurately detecting transcription start sites (TSS) is a starting point for understanding gene transcription, and an important ingredient in a number of applications necessary for functional gene annotation, such as gene and operon predictions. Available methods for TSS detection in bacteria use very different description of the bacterial promoter structure and all of them show low accuracy. It is therefore unclear which promoter features should be included in TSS recognition, and how their accuracy impacts the search detection. We here address this question for [Formula: see text] and [Formula: see text] (an alternative [Formula: see text] factor) promoters in E. coli. We find that [Formula: see text]35 element, which is considered exchangeable, and is often not included in TSS search, contributes to the search accuracy equally (for [Formula: see text], or more (for [Formula: see text] than the ubiquitous [Formula: see text]10 element. Surprisingly, the sequence of the spacer between [Formula: see text]35 and [Formula: see text]10 promoter elements, which is commonly included in TSS detection, significantly decreases the search accuracy for [Formula: see text] promoters. However, the spacer sequence improves the search accuracy for [Formula: see text] promoters, which we attribute to a presence of sequence conservation. Overall, there is as much as [Formula: see text]50% false positive reduction for optimally implemented promoter features in [Formula: see text], underlying necessity for accurate promoter element alignments.