Marc Parisien¹ & François Major¹ :

The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data

 Nature 452, 51-55 (6 March 2008) | doi:10.1038/nature06684; Received 7 January 2007; Accepted 11 January 2008

Zasha Weinberg, Jeffrey E. Barrick, Zizhen Yao, Adam Roth, Jane N. Kim, Jeremy Gore, Joy Xin Wang, Elaine R. Lee, Kirsten F. Block, Narasimhan Sudarsan, Shane Neph, Martin Tompa, Walter L. Ruzzo and Ronald R. Breaker: "Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline," Nucleic Acids Research Advance Access published July 9, 2007, doi:10.1093/nar/gkm487. PDF

Zizhen Yao,1 Jeffrey Barrick, Zasha Weinberg, Shane Neph, Ronald Breaker, Martin Tompa, and Walter L Ruzzo: "A Computational Pipeline for High- Throughput Discovery of cis-Regulatory Noncoding RNA in Prokaryotes," PLoS Comput Biol. 2007 July; 3(7): e126. Published online 2007 July 6. doi: 10.1371/journal.pcbi.0030126. Online

[FOLDALIGNM] Elfar Torarinsson, Jakob H. Havgaard, and Jan Gorodkin: "Multiple structural alignment and clustering of RNA sequences," Bioinformatics, 15 April 2007; 23: 926 - 932. PDF

[RNA Sampler] Xing Xu, Yongmei Ji, and Gary D. Stormo: "RNA Sampler: A new sampling based algorithm for common RNA secondary structure prediction and structural alignment," Bioinformatics, Advance Access published on May 30, 2007; doi: doi:10.1093/bioinformatics/btm272 PDF

[STRAL] Deniz Dalli, Andreas Wilm, Indra Mainz, and Gerhard Steger: "STRAL: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time," Bioinformatics, 1 July 2006; 22: 1593 - 1599. PDF

[lara] Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization
Markus Bauer, Gunnar W Klau, Knut Reinert
BMC Bioinformatics 2007, 8:271 (27 July 2007)

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