Smolke:Tech 21Dec06

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Tech talk references: 21 December 2006 Presenter: Chase RNA secondary structure prediction Eddy SR. How do RNA folding algorithms work?. Nat Biotechnol. 2004 Nov;22(11):1457-8. DOI:10.1038/nbt1104-1457 | Draper DE. A guide to ions and RNA structure. RNA. 2004 Mar;10(3):335-43. DOI:10.1261/rna.5205404 | Grilley D, Soto AM, and Draper DE. Mg2+-RNA interaction free energies and their relationship to the folding of RNA tertiary structures. Proc Natl Acad Sci U S A. 2006 Sep 19;103(38):14003-8. DOI:10.1073/pnas.0606409103 | Pan T and Sosnick T. RNA folding during transcription. Annu Rev Biophys Biomol Struct. 2006;35:161-75. DOI:10.1146/annurev.biophys.35.040405.102053 | Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, and Turner DH. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci U S A. 2004 May 11;101(19):7287-92. DOI:10.1073/pnas.0401799101 | Mathews DH. Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization. RNA. 2004 Aug;10(8):1178-90. DOI:10.1261/rna.7650904 | Mathews DH. Predicting a set of minimal free energy RNA secondary structures common to two sequences. Bioinformatics. 2005 May 15;21(10):2246-53. DOI:10.1093/bioinformatics/bti349 | Mathews DH and Turner DH. Prediction of RNA secondary structure by free energy minimization. Curr Opin Struct Biol. 2006 Jun;16(3):270-8. DOI:10.1016/j.sbi.2006.05.010 |