Journal article

Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes

Dennis K Gascoigne, Seth W Cheetham, Pierre B Cattenoz, Michael B Clark, Paulo P Amaral, Ryan J Taft, Dagmar Wilhelm, Marcel E Dinger, John S Mattick

Bioinformatics | OXFORD UNIV PRESS | Published : 2012

Abstract

MOTIVATION: Comparing transcriptomic data with proteomic data to identify protein-coding sequences is a long-standing challenge in molecular biology, one that is exacerbated by the increasing size of high-throughput datasets. To address this challenge, and thereby to improve the quality of genome annotation and understanding of genome biology, we have developed an integrated suite of programs, called Pinstripe. We demonstrate its application, utility and discovery power using transcriptomic and proteomic data from publicly available datasets. RESULTS: To demonstrate the efficacy of Pinstripe for large-scale analysis, we applied Pinstripe's reverse peptide mapping pipeline to a transcript lib..

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