title: Computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data.
abstract: High-throughput sequencing has been used to probe RNA structures, by treating RNAs with reagents that preferentially cleave or mark certain nucleotides according to their local structures, followed by sequencing of the resulting fragments. The data produced contain valuable information for studying various RNA properties.
  
  
  
  We developed methods for statistically modeling these structure-probing data and extracting structural features from them. We show that the extracted features can be used to predict RNA 'zipcodes' in yeast, regions bound by the She complex in asymmetric localization. The prediction accuracy was better than using raw RNA probing data or sequence features. We further demonstrate the use of the extracted features in identifying binding sites of RNA binding proteins from whole-transcriptome global photoactivatable-ribonucleoside-enhanced cross-linking and immunopurification (gPAR-CLIP) data.
  
  
  
  The source code of our implemented methods is available at http://yiplab.cse.cuhk.edu.hk/probrna/ CONTACT: kevinyip@cse.cuhk.edu.hk Supplementary information: Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong, CSIRO Ecosystem Sciences, Canberra, ACT 2601, Australia, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China 100084, School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong and Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong.
authors.forename: Xihao
authors.initials: X
authors.lastname: Hu
authors.affiliation: Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong, CSIRO Ecosystem Sciences, Canberra, ACT 2601, Australia, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China 100084, School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong and Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong, CSIRO Ecosystem Sciences, Canberra, ACT 2601, Australia, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China 100084, School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong and Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong.
authors.forename: Thomas K F
authors.initials: TK
authors.lastname: Wong
authors.affiliation: Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong, CSIRO Ecosystem Sciences, Canberra, ACT 2601, Australia, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China 100084, School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong and Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong.
authors.forename: Zhi John
authors.initials: ZJ
authors.lastname: Lu
authors.affiliation: Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong, CSIRO Ecosystem Sciences, Canberra, ACT 2601, Australia, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China 100084, School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong and Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong, CSIRO Ecosystem Sciences, Canberra, ACT 2601, Australia, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China 100084, School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong and Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong.
authors.forename: Ting Fung
authors.initials: TF
authors.lastname: Chan
authors.affiliation: Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong, CSIRO Ecosystem Sciences, Canberra, ACT 2601, Australia, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China 100084, School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong and Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong.
authors.forename: Terrence Chi Kong
authors.initials: TC
authors.lastname: Lau
authors.affiliation: Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong, CSIRO Ecosystem Sciences, Canberra, ACT 2601, Australia, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China 100084, School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong and Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong.
authors.forename: Siu Ming
authors.initials: SM
authors.lastname: Yiu
authors.affiliation: Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong, CSIRO Ecosystem Sciences, Canberra, ACT 2601, Australia, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China 100084, School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong and Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong, CSIRO Ecosystem Sciences, Canberra, ACT 2601, Australia, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China 100084, School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong and Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong.
authors.forename: Kevin Y
authors.initials: KY
authors.lastname: Yip
mesh_terms: D001665:Binding Sites; D019295:Computational Biology; D059014:High-Throughput Nucleotide Sequencing; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D012313:RNA / Q000737:chemistry*; D016601:RNA-Binding Proteins / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods; D059467:Transcriptome
chemical_list: D016601:RNA-Binding Proteins; D012313:RNA