GTfold: Enabling parallel RNA secondary structure prediction on multi-core desktops
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Zsuzsanna Sükösd | Stephen C Harvey | David A Bader | Andrew Ash | Joshua Anderson | M Shel Swenson | Prashant Gaurav | Christine E Heitsch
[1] Bruce A. Shapiro,et al. Optimization of an RNA Folding Algorithm for Parallel Architectures , 1998, Parallel Comput..
[2] Robert Giegerich,et al. A comprehensive comparison of comparative RNA structure prediction approaches , 2004, BMC Bioinformatics.
[3] J. Sabina,et al. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. , 1999, Journal of molecular biology.
[4] Michael Zuker,et al. UNAFold: software for nucleic acid folding and hybridization. , 2008, Methods in molecular biology.
[5] David A. Bader,et al. GTfold: a scalable multicore code for RNA secondary structure prediction , 2009, SAC '09.
[6] J. McCaskill. The equilibrium partition function and base pair binding probabilities for RNA secondary structure , 1990, Biopolymers.
[7] David H. Mathews,et al. NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure , 2009, Nucleic Acids Res..
[8] Peter F. Stadler,et al. Knowledge Discovery in RNA Sequence Families of HIV Using Scalable Computers , 1996, KDD.
[9] D. Mathews,et al. Accurate SHAPE-directed RNA structure determination , 2009, Proceedings of the National Academy of Sciences.
[10] Michael Zuker,et al. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information , 1981, Nucleic Acids Res..
[11] Nan Yu,et al. The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs , 2002, BMC Bioinformatics.
[12] D. Turner,et al. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[13] Daniel A. Keim,et al. On Knowledge Discovery and Data Mining , 1997 .
[14] Peter F. Stadler,et al. Prediction of RNA Base Pairing Probabilities on Massively Parallel Computers , 2000, J. Comput. Biol..
[15] P. Schuster,et al. Complete suboptimal folding of RNA and the stability of secondary structures. , 1999, Biopolymers.
[16] David A. Bader,et al. Algorithm Engineering for Parallel Computation , 2000, Experimental Algorithmics.
[17] Walter Fontana,et al. Fast folding and comparison of RNA secondary structures , 1994 .
[18] Christian N. S. Pedersen,et al. Internal loops in RNA secondary structure prediction , 1999, RECOMB.
[19] R. Gutell,et al. The accuracy of ribosomal RNA comparative structure models. , 2002, Current opinion in structural biology.
[20] Peter F. Stadler,et al. Memory Efficient Folding Algorithms for Circular RNA Secondary Structures , 2006, German Conference on Bioinformatics.