title: Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures.
abstract: T-Coffee (Tree-based consistency objective function for alignment evaluation) is a versatile multiple sequence alignment (MSA) method suitable for aligning most types of biological sequences. The main strength of T-Coffee is its ability to combine third party aligners and to integrate structural (or homology) information when building MSAs. The series of protocols presented here show how the package can be used to multiply align proteins, RNA and DNA sequences. The protein section shows how users can select the most suitable T-Coffee mode for their data set. Detailed protocols include T-Coffee, the default mode, M-Coffee, a meta version able to combine several third party aligners into one, PSI (position-specific iterated)-Coffee, the homology extended mode suitable for remote homologs and Expresso, the structure-based multiple aligner. We then also show how the T-RMSD (tree based on root mean square deviation) option can be used to produce a functionally informative structure-based clustering. RNA alignment procedures are described for using R-Coffee, a mode able to use predicted RNA secondary structures when aligning RNA sequences. DNA alignments are illustrated with Pro-Coffee, a multiple aligner specific of promoter regions. We also present some of the many reformatting utilities bundled with T-Coffee. The package is an open-source freeware available from http://www.tcoffee.org/.
authors: Comparative Bioinformatics Group, Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra, Barcelona, Spain.
authors: Jean-Francois
authors: JF
authors: Taly
authors: Cedrik
authors: C
authors: Magis
authors: Giovanni
authors: G
authors: Bussotti
authors: Jia-Ming
authors: JM
authors: Chang
authors: Paolo
authors: P
authors: Di Tommaso
authors: Ionas
authors: I
authors: Erb
authors: Jose
authors: J
authors: Espinosa-Carrasco
authors: Carsten
authors: C
authors: Kemena
authors: Cedric
authors: C
authors: Notredame
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011506:Proteins / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins; D012313:RNA; D004247:DNA