SCOPE++: sequence classification of homoPolymer emissions.

ABSTRACT:

Background

mRNA polyadenylation, the addition of a poly(A) tail to the 3'-end of pre-mRNA, is a process critical to gene expression and regulation in eukaryotes. To understand the molecular mechanisms governing polyadenylation and other relevant biological processes, it is important to identify these poly(A) tails accurately in transcriptome sequencing data and differentiate them from artificial adapter sequences added in the sequencing process. But the annotation of these tails is complicated by the presence of sequencing errors and post-transcriptional modifications. While determining that a tail is present in a given transcript fragment is straight-forward, these obfuscations make the problem of boundary identification a challenge; conventional seed-and-extend algorithms struggl

SUBMITTER: Morton JT 

PROVIDER: S-EPMC4165746 | biostudies-literature | 2014 Sep

REPOSITORIES: biostudies-literature