Introduction

More than half of human genes exercise alternative polyadenylation (APA) and generate mRNA transcripts with varying 3' untranslated regions (UTR). The increasing significance of APA in cancer and neurological disease has propelled the development of several 3’ sequencing (3’Seq) techniques. In spite of the recent data explosion, there are no computational tools that are precisely designed for 3’Seq data. PolyA-miner is the first computational tool developed specifically for 3’Seq data. PolyA-miner can effectively identify novel APA sites that are otherwise undetected using reference-based approaches.It accounts for non-proximal to non-distal APA switches using vector projections and is less susceptible to inherent data variations. With the emerging importance of alternative polyadenylation in studying human diseases, PolyA-miner can significantly accelerate analysis and help decoding the missing pieces of underlying alternative polyadenylation dynamics.