Poster: Sequence classification of homopolymer emissions (SCOPE)

In this poster we will describe SCOPE: a tool for the identification and removal of homopolymer sequences embedded in sequenced mRNA transcript fragments as a result of the Eukaryotic polyadenylation process, allowing for the identification and cleaning of next generation sequence transcriptome data of fragments added by post-transcriptional processes. By making use of Hidden Markov models trained on-the-fly we are able to detect the embedded homopolymers and accurately identify boundaries in the presence of high rates of sequencing error that might otherwise obscure them. Compared to the SeqClean tool [1], we see comparable to considerably improved sensitivity and specificity in identification, and a significantly improved ability to correctly detect homopolymer boundaries. SCOPE is being developed as an open-source tool, with a preliminary version that will be distributed to interested users upon request to the authors.