PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration.

ABSTRACT: An increasing amount of studies integrate mRNA sequencing data into MS-based proteomics to complement the translation product search space. However, several factors, including extensive regulation of mRNA translation and the need for three- or six-frame-translation, impede the use of mRNA-seq data for the construction of a protein sequence search database. With that in mind, we developed the PROTEOFORMER tool that automatically processes data of the recently developed ribosome profiling method (sequencing of ribosome-protected mRNA fragments), resulting in genome-wide visualization of ribosome occupancy. Our tool also includes a translation initiation site calling algorithm allowing the delineation of the open reading frames (ORFs) of all translation products. A complete protein synthesis-

SUBMITTER: Crappe J 

PROVIDER: S-EPMC4357689 | biostudies-literature | 2015 Mar

REPOSITORIES: biostudies-literature