R-Coffee is a package for multiple RNA sequence alignments, derived from T-Coffee package. It uses structural information in the construction of the sequence alignments and a special version of T-Coffee constructs the multiple sequence alignments incorporating the structural information. Requirements: RNAlpfold from the Vienna package, Mafft, Muscle, ProbCons, and ConSan.
Functional, regulatory and non-coding RNA; Nucleic acid structure analysis; Structure prediction; RNA; Sequence analysis
Wilm A, Higgins DG, Notredame C "R-Coffee: a method for multiple alignment of non-coding RNA." Nucleic Acids Res. 2008 May;36(9):e52. https://doi.org/10.1093/nar/gkn174
PMID: 18420654
PMCID: PMC2396437
Moretti S, Wilm A, Higgins DG, Xenarios I, Notredame C "R-Coffee: a web server for accurately aligning noncoding RNA sequences." Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W10-3. doi: 10.1093/nar/gkn278. Epub 2008 May 15. https://doi.org/10.1093/nar/gkn278
PMID: 18483080
PMCID: PMC2447777
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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