IRESite--a tool for the examination of viral and cellular internal ribosome entry sites.
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.
Mokrejs
Martin
M
Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Vinicná 5, 128 44 Prague 2, Czech Republic. martin@natur.cuni.cz
Masek
Tomás
T
Vopálensky
Václav
V
Hlubucek
Petr
P
Delbos
Philippe
P
Pospísek
Martin
M
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
D012367:RNA, Viral