MOTIVATION: The length of the 3' untranslated region (3' UTR) of an mRNA is 
essential for many biological activities such as mRNA stability, sub-cellular 
localization, protein translation, protein binding and translation efficiency. 
Moreover, correlation between diseases and the shortening (or lengthening) of 3' 
UTRs has been reported in the literature. This length is largely determined by 
the polyadenylation cleavage site in the mRNA. As alternative polyadenylation 
(APA) sites are common in mammalian genes, several tools have been published 
recently for detecting APA sites from RNA-Seq data or performing 
shortening/lengthening analysis. These tools consider either up to only two APA 
sites in a gene or only APA sites that occur in the last exon of a gene, 
although a gene may generally have more than two APA sites and an APA site may 
sometimes occur before the last exon. Furthermore, the tools are unable to 
integrate the analysis of shortening/lengthening events with APA site detection.
RESULTS: We propose a new tool, called TAPAS, for detecting novel APA sites from 
RNA-Seq data. It can deal with more than two APA sites in a gene as well as APA 
sites that occur before the last exon. The tool is based on an existing method 
for finding change points in time series data, but some filtration techniques 
are also adopted to remove change points that are likely false APA sites. It is 
then extended to identify APA sites that are expressed differently between two 
biological samples and genes that contain 3' UTRs with shortening/lengthening 
events. Our extensive experiments on simulated and real RNA-Seq data demonstrate 
that TAPAS outperforms the existing tools for APA site detection or 
shortening/lengthening analysis significantly.
AVAILABILITY AND IMPLEMENTATION: https://github.com/arefeen/TAPAS.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics 
online.