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AUTHORS
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Some Perl written by Ashton Trey Belew <abelew@gmail.com>
Jonathan Jacobs wrote the original version
Nic Hepler wrote the original PRFSNP.pm
Nupack:
R.M. Dirks, J.S. Bois, J.M. Schaeffer, E. Winfree, and N.A. Pierce. (2007)
Thermodynamic analysis of interacting nucleic acid strands. SIAM Rev, 49, 65-88.
Pknots:
E. Rivas, S.R. Eddy (1999)
A dynamic programming algorithm for RNA structure prediction including pseudoknots. J Mol Biol. Feb 5;285(5):2053-68.
Hotknots:
Ren, J., Rastegari, B., Condon, A., and Hoos, H. H. (2005).
HotKnots: heuristic prediction of RNA secondary structures including pseudoknots. RNA, 11(10), 1494--1504.
Andronescu, M., Pop, C., and Condon, A. (2010)
Improved energy parameters for RNA pseudoknotted secondary structure prediction, RNA. Jan;16(1):26-42.
mfold:
M. Zuker. (1994)
Prediction of RNA Secondary Structure by Energy Minimization. In Computer Analysis of Sequence Data... , 267-294
Among many other references...
Unafold:
This is the continuation of mfold and was written by Nicholas Markham and Michael Zuker.
DINAMelt web server for nucleic acid melting prediction. NAR. 33:W577-W581. (2003)
RNAhybrid:
Marc Rehmsmeier, Peter Steffen, Matthias Höchsmann, Robert Giegerich (2004)
Fast and effective prediction of microRNA/target duplexes RNA, 10:1507-1517
rnamotif:
T. Macke, D. Ecker, R. Gutell, D. Gautheret, D.A. Case and R. Sampath. (2001)
RNAMotif -- A new RNA secondary structure definition and discovery algorithm. Nucl. Acids Res. 29, 4724-4735
Vienna:
Ivo L. Hofacker, Walter Fontana, Peter F. Stadler, Sebastian Bonhoeffer, Manfred Tacker, and Peter Schuster. (1994)
Fast folding and comparison of RNA secondary structures (the Vienna RNA Package). Monatsh. Chem., 125(2):167–188
miRanda
John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS., (2008)
Human MicroRNA targets. PLoS Biol. 2005 Jul;3(7):e264.
BLAST
Altschul SF; Gish W; Miller W; Myers EW; Lipman DJ (1990)
Basic local alignment search tool. J Mol Biol 215: 403-10
jViz.RNA
http://jviz.cs.sfu.ca/
Kay C. Wiese and Edward Glen (2006)
"jViz.Rna - An Interactive Graphical Tool for Visualizing RNA Secondary Structure Including Pseudoknots",
Proceedings of the 19th International Symposium on Computer Based Medical Systems
(IEEE/CBMS-2006), June 2006, pp 659-664.
Bioperl
Copyright (c) 1996-2009 Georg Fuellen, Richard Resnick, Steven E. Brenner, Chris
Dagdigian, Steve Chervitz, Ewan Birney, James Gilbert, Elia Stupka, and others.
HTML::Mason
http://www.masonhq.com