TECtool (Terminal Exon Characterization tool) is a machine learning-based annotation software (implemented in Python) that makes use of RNA sequencing (RNA-seq) data to identify novel terminal exons, infer novel transcript isoforms and annotate potential coding sequences.
The KAPAC tool enables the identification of sequence motifs that can explain changes in cellular 3' end processing from high-throughput sequencing data.
PAQR, standing for polyadenylation site usage quantification from RNA sequencing data, allows to quantify 3' end usage from standard RNA sequencing libraries.