title: aPPRove: An HMM-Based Method for Accurate Prediction of RNA-Pentatricopeptide Repeat Protein Binding Events.
abstract: Pentatricopeptide repeat containing proteins (PPRs) bind to RNA transcripts originating from mitochondria and plastids. There are two classes of PPR proteins. The [Formula: see text] class contains tandem [Formula: see text]-type motif sequences, and the [Formula: see text] class contains alternating [Formula: see text], [Formula: see text] and [Formula: see text] type sequences. In this paper, we describe a novel tool that predicts PPR-RNA interaction; specifically, our method, which we call aPPRove, determines where and how a [Formula: see text]-class PPR protein will bind to RNA when given a PPR and one or more RNA transcripts by using a combinatorial binding code for site specificity proposed by Barkan et al. Our results demonstrate that aPPRove successfully locates how and where a PPR protein belonging to the [Formula: see text] class can bind to RNA. For each binding event it outputs the binding site, the amino-acid-nucleotide interaction, and its statistical significance. Furthermore, we show that our method can be used to predict binding events for [Formula: see text]-class proteins using a known edit site and the statistical significance of aligning the PPR protein to that site. In particular, we use our method to make a conjecture regarding an interaction between CLB19 and the second intronic region of ycf3. The aPPRove web server can be found at www.cs.colostate.edu/~approve.
authors: Department of Computer Science, Colorado State University, Fort Collins, CO, 80523, United States of America.
authors: Thomas
authors: T
authors: Harrison
authors: Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, 32611, United States of America.
authors: Jaime
authors: J
authors: Ruiz
authors: Department of Biology, Colorado State University, Fort Collins, CO, 80523, United States of America.
authors: Daniel B
authors: DB
authors: Sloan
authors: Department of Computer Science, Colorado State University, Fort Collins, CO, 80523, United States of America.
authors: Asa
authors: A
authors: Ben-Hur
authors: Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, 32611, United States of America.
authors: Christina
authors: C
authors: Boucher
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001665:Binding Sites / Q000235:genetics; D060365:Chloroplast Proteins / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D020407:Internet; D008390:Markov Chains; D024101:Mitochondrial Proteins / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D012313:RNA / Q000235:genetics / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid
chemical_list: D060365:Chloroplast Proteins; D024101:Mitochondrial Proteins; D016601:RNA-Binding Proteins; D012313:RNA