PSI-Coffee is a part of the T-Coffe distribution and specifically designed for making multiple sequence alignments (MSAs) of alpha-helical transmembrane protein sequences. The Authors claim PSI-Coffee to be more accurate than MSAProbs, Kalign, PROMALS, MAFFT, ProbCons, and PRALINE.
Phylogeny; Sequence analysis; Nucleic acid sites, features and motifs; Nucleic acid structure analysis; Sequence sites, features and motifs
Chang JM, Di Tommaso P, Taly JF, Notredame C "Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee." BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S1. https://doi.org/10.1186/1471-2105-13-S4-S1
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
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
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
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