APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins.
RNA-binding proteins (RBPs) have been established as core components of several post-transcriptional gene regulation mechanisms. Experimental techniques such as cross-linking and co-immunoprecipitation have enabled the identification of RBPs, RNA-binding domains (RBDs) and their regulatory roles in the eukaryotic species such as human and yeast in large-scale. In contrast, our knowledge of the number and potential diversity of RBPs in bacteria is poorer due to the technical challenges associated with the existing global screening approaches. We introduce APRICOT, a computational pipeline for the sequence-based identification and characterization of proteins using RBDs known from experimental studies. The pipeline identifies functional motifs in protein sequences using position-specific scoring matrices and Hidden Markov Models of the functional domains and statistically scores them based on a series of sequence-based features. Subsequently, APRICOT identifies putative RBPs and characterizes them by several biological properties. Here we demonstrate the application and adaptability of the pipeline on large-scale protein sets, including the bacterial proteome of Escherichia coli. APRICOT showed better performance on various datasets compared to other existing tools for the sequence-based prediction of RBPs by achieving an average sensitivity and specificity of 0.90 and 0.91 respectively. The command-line tool and its documentation are available at https://pypi.python.org/pypi/bio-apricot.
Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany.
Malvika
M
Sharan
Core Unit Systems Medicine, University of Würzburg, 97080 Würzburg, Germany.
Konrad U
KU
Förstner
Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany.
Ana
A
Eulalio
Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany.
Jörg
J
Vogel
D001665:Binding Sites; D019295:Computational Biology; D029968:Escherichia coli Proteins / Q000737:chemistry; D058977:Molecular Sequence Annotation; D000072417:Protein Domains; D016601:RNA-Binding Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein; D012984:Software
D029968:Escherichia coli Proteins; D016601:RNA-Binding Proteins