title: Impact of RNA structure on the prediction of donor and acceptor splice sites.
abstract: BACKGROUND
  gene identification in genomic DNA sequences by computational methods has become an important task in bioinformatics and computational gene prediction tools are now essential components of every genome sequencing project. Prediction of splice sites is a key step of all gene structural prediction algorithms.
  
  
  RESULTS
  we sought the role of mRNA secondary structures and their information contents for five vertebrate and plant splice site datasets. We selected 900-nucleotide sequences centered at each (real or decoy) donor and acceptor sites, and predicted their corresponding RNA structures by Vienna software. Then, based on whether the nucleotide is in a stem or not, the conventional four-letter nucleotide alphabet was translated into an eight-letter alphabet. Zero-, first- and second-order Markov models were selected as the signal detection methods. It is shown that applying the eight-letter alphabet compared to the four-letter alphabet considerably increases the accuracy of both donor and acceptor site predictions in case of higher order Markov models.
  
  
  CONCLUSIONS
  Our results imply that RNA structure contains important data and future gene prediction programs can take advantage of such information.
authors.affiliation: Department of Biotechnology, University College of Science, University of Tehran, Tehran, Iran. marashie@khayam.ut.ac.ir
authors.forename: Sayed-Amir
authors.initials: SA
authors.lastname: Marashi
authors.forename: Changiz
authors.initials: C
authors.lastname: Eslahchi
authors.forename: Hamid
authors.initials: H
authors.lastname: Pezeshk
authors.forename: Mehdi
authors.initials: M
authors.lastname: Sadeghi
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D006801:Humans; D016013:Likelihood Functions; D008390:Markov Chains; D008957:Models, Genetic; D009690:Nucleic Acid Conformation; D022821:RNA Splice Sites; D012326:RNA Splicing; D012333:RNA, Messenger / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods; D012984:Software
chemical_list: D022821:RNA Splice Sites; D012333:RNA, Messenger; D018749:RNA, Plant