Accurate identification of polyadenylation sites from 3' end deep sequencing using a naive Bayes classifier.

ABSTRACT:

Motivation

3' end processing is important for transcription termination, mRNA stability and regulation of gene expression. To identify 3' ends, most techniques use an oligo-dT primer to construct deep sequencing libraries. However, this approach can lead to identification of artifactual polyadenylation sites due to internal priming in homopolymeric stretches of adenines. Although heuristic filters have been applied in these cases, they typically result in a high proportion of both false-positive and -negative classifications. Therefore, there is a need to develop improved algorithms to better identify mis-priming events in oligo-dT primed sequences.

Results

By analyzing sequence features flanking 3' ends derived from oligo-dT-based sequencing, we developed a naïve Bayes clas

SUBMITTER: Sheppard S 

PROVIDER: S-EPMC3789547 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature