Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment

Sundfeld D, Havgaard JH, de Melo AC, Gorodkin J* Bioinformatics. 2016 Apr 15;32(8):1238-40. Epub 2015 Dec 24
[ PubMed | Paper | Webserver | Software ]

Comparative ncRNA gene and structure prediction using Foldalign and FoldalignM

Havgaard J, Kaur S, Gorodkin J* Curr Protoc Bioinformatics. 2012 Sep;Chapter 12:12.11.1-12.11.15
[ PubMed | Chapter ]

Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix

Havgaard JH, Torarinsson E, Gorodkin J* PLoS Comput Biol. 2007 Oct;3(10):1896-908. Epub 2007 Aug 20
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Multiple structural alignment and clustering of RNA sequences

Torarinsson E, Havgaard JH, Gorodkin J* Bioinformatics. 2007 Apr 15;23(8):926-32. Epub 2007 Feb 25
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The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search

Havgaard JH, Lyngso RB, Gorodkin J* Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W650-3
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Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%

Havgaard JH*, Lyngso RB, Stormo GD, Gorodkin J Bioinformatics. 2005 May 1;21(9):1815-24. Epub 2005 Jan 18
[ PubMed | Paper ]