title: PPUS: a web server to predict PUS-specific pseudouridine sites.
abstract: BACKGROUND
  Pseudouridine (Ψ), catalyzed by pseudouridine synthase (PUS), is the most abundant RNA modification and has important cellular functions. Developing an algorithm to identify Ψ sites is an important work. And it is better if the algorithm could assign which PUS modifies the Ψ sites. Here, we developed PPUS (http://lyh.pkmu.cn/ppus/), the first web server to predict PUS-specific Ψ sites. PPUS: employed support vector machine as the classifier and used nucleotides around Ψ sites as the features. Currently, PPUS: could accurately predict new Ψ sites for PUS1, PUS4 and PUS7 in yeast and PUS4 in human. PPUS: is well designed and friendly to user.
  
  
  METHODS
  Our web server is available freely for non-commercial purposes at: http://lyh.pkmu.cn/ppus/
  
  
  BACKGROUND
  liyanhui@bjmu.edu.cn or cuiqinghua@hsc.pku.edu.cn.
authors.affiliation: Institute of Cardiovascular Sciences, Peking University Health Science Center.
authors.forename: Yan-Hui
authors.initials: YH
authors.lastname: Li
authors.affiliation: Department of Geriatrics and Gerontology, Beijing Huaxin Hospital, the First Affiliated Hospital of Tsinghua University and.
authors.forename: Gaigai
authors.initials: G
authors.lastname: Zhang
authors.affiliation: Department of Biomedical Informatics, Peking University Health Science Center, Beijing, China.
authors.forename: Qinghua
authors.initials: Q
authors.lastname: Cui
mesh_terms: D000465:Algorithms; D006801:Humans; D020407:Internet; D019751:Intramolecular Transferases / Q000378:metabolism*; D011560:Pseudouridine / Q000032:analysis* / Q000378:metabolism; D012343:RNA, Transfer / Q000737:chemistry / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000201:enzymology / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D060388:Support Vector Machine
chemical_list: C474390:Pus7 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D011560:Pseudouridine; D012343:RNA, Transfer; D019751:Intramolecular Transferases; C096995:pseudouridine synthases; C023199:tRNA-pseudouridine synthase I