Shoelaces: an interactive tool for ribosome profiling processing and visualization.

ABSTRACT:

Background

The emergence of ribosome profiling to map actively translating ribosomes has laid the foundation for a diverse range of studies on translational regulation. The data obtained with different variations of this assay is typically manually processed, which has created a need for tools that would streamline and standardize processing steps.

Results

We present Shoelaces, a toolkit for ribosome profiling experiments automating read selection and filtering to obtain genuine translating footprints. Based on periodicity, favoring enrichment over the coding regions, it determines the read lengths corresponding to bona fide ribosome protected fragments. The specific codon under translation (P-site) is determined by automatic offset calculations resulting in sub-codon resolu

SUBMITTER: Birkeland A 

PROVIDER: S-EPMC6052522 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature