title: IRESite--a tool for the examination of viral and cellular internal ribosome entry sites.
abstract: The IRESite (http://www.iresite.org) presents carefully curated experimental evidence of many eukaryotic viral and cellular internal ribosome entry site (IRES) regions. At the time of submission, IRESite stored >600 records. The IRESite gradually evolved into a robust tool providing (i) biologically meaningful information regarding the IRESs and their experimental background (including annotation of IRES secondary structures and IRES trans-acting factors) as well as (ii) thorough concluding remarks to stored database entries and regularly updated evaluation of the reported IRES function. A substantial portion of the IRESite data results purely from in-house bioinformatic analyses of currently available sequences, in silico attempts to repeat published cloning experiments, DNA sequencing and restriction endonuclease verification of received plasmid DNA. We also present a newly implemented tool for displaying RNA secondary structures and for searching through the structures currently stored in the database. The supplementary material contains an updated list of reported IRESs.
authors.affiliation: Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Vinicná 5, 128 44 Prague 2, Czech Republic. martin@natur.cuni.cz
authors.forename: Martin
authors.initials: M
authors.lastname: Mokrejs
authors.forename: Tomás
authors.initials: T
authors.lastname: Masek
authors.forename: Václav
authors.initials: V
authors.lastname: Vopálensky
authors.forename: Petr
authors.initials: P
authors.lastname: Hlubucek
authors.forename: Philippe
authors.initials: P
authors.lastname: Delbos
authors.forename: Martin
authors.initials: M
authors.lastname: Pospísek
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods* / Q000639:trends; D030541:Databases, Genetic; D030561:Databases, Nucleic Acid; D016679:Genome, Viral; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D020407:Internet; D009690:Nucleic Acid Conformation; D010442:Peptide Chain Initiation, Translational / Q000235:genetics; D010957:Plasmids / Q000378:metabolism; D012367:RNA, Viral / Q000235:genetics*; D012270:Ribosomes / Q000235:genetics*; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D012367:RNA, Viral