Comparison of approaches for rational siRNA design leading to a new efficient and transparent method

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  author =       "Olga Matveeva and Yury Nechipurenko and Leo Rossi and 
                 Barry Moore and Pal Saetrom and Aleksey Y. Ogurtsov and 
                 John F. Atkins and Svetlana A. Shabalina",
  title =        "Comparison of approaches for rational siRNA design
                 leading to a new efficient and transparent method",
  journal =      "Nucleic Acids Research",
  year =         "2007",
  volume =       "35",
  number =       "8",
  pages =        "e63",
  month =        apr,
  keywords =     "genetic algorithms, genetic programming",
  DOI =          "doi:10.1093/nar/gkm088",
  abstract =     "Current literature describes several methods for the
                 design of efficient siRNAs with 19 perfectly matched
                 base pairs and 2 nt overhangs. Using four independent
                 databases totaling 3336 experimentally verified siRNAs,
                 we compared how well several of these methods predict
                 siRNA cleavage efficiency. According to receiver
                 operating characteristics (ROC) and correlation
                 analyses, the best programs were BioPredsi,
                 ThermoComposition and DSIR. We also studied individual
                 parameters that significantly and consistently
                 correlated with siRNA efficacy in different databases.
                 As a result of this work we developed a new method
                 which uses linear regression fitting with local duplex
                 stability, nucleotide position-dependent preferences
                 and total G/C content of siRNA duplexes as input
                 parameters. The new method's discrimination ability of
                 efficient and inefficient siRNAs is comparable with
                 that of the best methods identified, but its parameters
                 are more obviously related to the mechanisms of siRNA
                 action in comparison with BioPredsi. This permits
                 insight to the underlying physical features and
                 relative importance of the parameters. The new method
                 of predicting siRNA efficiency is faster than that of
                 ThermoComposition because it does not employ
                 time-consuming RNA secondary structure calculations and
                 has much less parameters than DSIR. It is available as
                 a web tool called siRNA scales.",
  notes =        "PMID: 4 methods, including \cite{Saetrom:2004:BI}

Genetic Programming entries for Olga Matveeva Yury Nechipurenko Leo Rossi Barry Moore Pal Saetrom Aleksey Y Ogurtsov John F Atkins Svetlana A Shabalina