Searching for IRES

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@Article{Baird:2006:RNA,
  author =       "Stephen D. Baird and Marcel Turcotte and 
                 Robert G. Korneluk and Martin Holcik",
  title =        "Searching for IRES",
  journal =      "RNA",
  year =         "2006",
  volume =       "12",
  number =       "10",
  pages =        "1755--1785",
  month =        oct,
  publisher =    "RNA Society",
  keywords =     "genetic algorithms, genetic programming, IRES, RNA,
                 secondary structure, prediction software",
  DOI =          "doi:10.1261/rna.157806",
  abstract =     "The cell has many ways to regulate the production of
                 proteins. One mechanism is through the changes to the
                 machinery of translation initiation. These alterations
                 favor the translation of one subset of mRNAs over
                 another. It was first shown that internal ribosome
                 entry sites (IRESes) within viral RNA genomes allowed
                 the production of viral proteins more efficiently than
                 most of the host proteins. The RNA secondary structure
                 of viral IRESes has sometimes been conserved between
                 viral species even though the primary sequences differ.
                 These structures are important for IRES function, but
                 no similar structure conservation has yet to be shown
                 in cellular IRES. With the advances in mathematical
                 modeling and computational approaches to complex
                 biological problems, is there a way to predict an IRES
                 in a data set of unknown sequences? This review
                 examines what is known about cellular IRES structures,
                 as well as the data sets and tools available to examine
                 this question. We find that the lengths, number of
                 upstream AUGs, and %GC content of 5'-UTRs of the human
                 transcriptome have a similar distribution to those of
                 published IRES-containing UTRs. Although the UTRs
                 containing IRESes are on the average longer, almost
                 half of all 5'-UTRs are long enough to contain an IRES.
                 Examination of the available RNA structure prediction
                 software and RNA motif searching programs indicates
                 that while these programs are useful tools to fine tune
                 the empirically determined RNA secondary structure, the
                 accuracy of de novo secondary structure prediction of
                 large RNA molecules and subsequent identification of
                 new IRES elements by computational approaches, is still
                 not possible.",
  notes =        "Paragraph on \cite{Yuh-JyhHu:2003:NAR} PMCID:
                 PMC1581980",
}

Genetic Programming entries for Stephen D Baird Marcel Turcotte Robert G Korneluk Martin Holcik

Citations