Mar 24, 2017

APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins

Nucleic Acids Research
Malvika SharanJörg Vogel

Abstract

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 datas...Continue Reading

Mentioned in this Paper

Transcription, Genetic
Yeasts
RNA Recognition Motif
Computer Programs and Programming
Proteome
Adaptation
Protein Domain
Screening Generic
Molecular Sequence Annotation
Base Sequence

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