DeepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns.

ABSTRACT:

Motivation

High-throughput sequencing methods allow whole transcriptomes to be sequenced fast and cost-effectively. Short RNA sequencing provides not only quantitative expression data but also an opportunity to identify novel coding and non-coding RNAs. Many long transcripts undergo post-transcriptional processing that generates short RNA sequence fragments. Mapped back to a reference genome, they form distinctive patterns that convey information on both the structure of the parent transcript and the modalities of its processing. The miR-miR* pattern from microRNA precursors is the best-known, but by no means singular, example.

Results

deepBlockAlign introduces a two-step approach to align RNA-seq read patterns with the aim of quickly identifying RNAs that share similar proc

SUBMITTER: Langenberger D 

PROVIDER: S-EPMC3244762 | biostudies-literature | 2012 Jan

REPOSITORIES: biostudies-literature