title: IRSS: a web-based tool for automatic layout and analysis of IRES secondary structure prediction and searching system in silico.
abstract: BACKGROUND
  Internal ribosomal entry sites (IRESs) provide alternative, cap-independent translation initiation sites in eukaryotic cells. IRES elements are important factors in viral genomes and are also useful tools for bi-cistronic expression vectors. Most existing RNA structure prediction programs are unable to deal with IRES elements.
  
  
  RESULTS
  We designed an IRES search system, named IRSS, to obtain better results for IRES prediction. RNA secondary structure prediction and comparison software programs were implemented to construct our two-stage strategy for the IRSS. Two software programs formed the backbone of IRSS: the RNAL fold program, used to predict local RNA secondary structures by minimum free energy method; and the RNA Align program, used to compare predicted structures. After complete viral genome database search, the IRSS have low error rate and up to 72.3% sensitivity in appropriated parameters.
  
  
  CONCLUSIONS
  IRSS is freely available at this website http://140.135.61.9/ires/. In addition, all source codes, precompiled binaries, examples and documentations are downloadable for local execution. This new search approach for IRES elements will provide a useful research tool on IRES related studies.
authors.affiliation: Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan. tywu@cycu.edu.tw
authors.forename: Tzong-Yuan
authors.initials: TY
authors.lastname: Wu
authors.forename: Chi-Chun
authors.initials: CC
authors.lastname: Hsieh
authors.forename: Jun-Jie
authors.initials: JJ
authors.lastname: Hong
authors.forename: Chung-Yung
authors.initials: CY
authors.lastname: Chen
authors.forename: Yuh-Show
authors.initials: YS
authors.lastname: Tsai
mesh_terms: D001483:Base Sequence; D003198:Computer Simulation; D016002:Discriminant Analysis; D016679:Genome, Viral; D020407:Internet; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012333:RNA, Messenger / Q000737:chemistry* / Q000235:genetics; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D013816:Thermodynamics; D014584:User-Computer Interface
chemical_list: D012333:RNA, Messenger; D012367:RNA, Viral