Topic

RNA-Seq; RNA; Sequence analysis

Details

Publications

Di Tommaso P, Bussotti G, Kemena C, Capriotti E, Chatzou M, Prieto P, Notredame C. "SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments." Nucleic Acids Res. 2014 Jul;42(Web Server issue):W356-60. https://doi.org/10.1093/nar/gku459
PMID: 24972831
PMCID: PMC4086076

Chew LP, Huttenlocher D, Kedem K, Kleinberg J "Fast detection of common geometric substructure in proteins." J Comput Biol. 1999 Fall-Winter;6(3-4):313-25. https://doi.org/10.1089/106652799318292
PMID: 10582569

Capriotti E, Marti-Renom MA "RNA structure alignment by a unit-vector approach." Bioinformatics. 2008 Aug 15;24(16):i112-8. https://doi.org/10.1093/bioinformatics/btn288
PMID: 18689811

Kemena C, Bussotti G, Capriotti E, Marti-Renom MA, Notredame C "Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package." Bioinformatics. 2013 May 1;29(9):1112-9. https://doi.org/10.1093/bioinformatics/btt096
PMID: 23449094

Notredame C, Higgins DG, Heringa J "T-Coffee: A novel method for fast and accurate multiple sequence alignment." J Mol Biol. 2000 Sep 8;302(1):205-17. https://doi.org/10.1006/jmbi.2000.4042
PMID: 10964570

Magis C, Taly JF, Bussotti G, Chang JM, Di Tommaso P, Erb I, Espinosa-Carrasco J, Notredame C "T-Coffee: Tree-based consistency objective function for alignment evaluation." Methods Mol Biol. 2014;1079:117-29. https://doi.org/10.1007/978-1-62703-646-7_7
PMID: 24170398

Taly JF, Magis C, Bussotti G, Chang JM, Di Tommaso P, Erb I, Espinosa-Carrasco J, Kemena C, Notredame C "Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures." Nat Protoc. 2011 Nov;6(11):1669-82. https://doi.org/10.1038/nprot.2011.393
PMID: 21979275

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