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Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures

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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/.

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Figure 1: Multiple sequence alignments of eight SH3 protein domains.
Figure 2: Structural classification of the cysteine-rich domain (CRD) family.
Figure 3: Comparison of T-Coffee and R-Coffee alignments.
Figure 4: Pro-Coffee: alignment of promoter regions using Pro-Coffee.

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Acknowledgements

We thank J. Ramón González-Vallinas and E. Eyras for providing ChIP-seq analysis used in Figure 4. This project is supported by the Plan Nacional BFU2008-00419, the LEISHDRUG (no. 223414) and the Quantomics (KBBE-2A-222664) projects of the 7th Framework Programme of the European Commission and by a 'la Caixa' International PhD Program fellowship. Computational resources are provided by the Center for Genomic Regulation (CRG) of Barcelona.

AUTHOR CONTRIBUTIONS

J.-F.T., C.M., J.-M.C. and C.N. conceived and executed the experiments about protein sequences and structures. G.B., C.K. and C.N. conceived and executed the experiments about RNA sequences. I.E. and C.N. conceived and executed the experiments about DNA sequences. P.D.T. and C.N. conceived and developed the installation procedure. J.-F.T., C.M., G.B., J.-M.C., P.D.T., I.E., J.E.-C., C.K. and C.N. wrote the manuscript.

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  1. Jean-Francois Taly and Cedrik Magis: These authors contributed equally to this work.

Authors and Affiliations

  1. Comparative Bioinformatics Group, Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra (UPF), Barcelona, Spain

    Jean-Francois Taly, Cedrik Magis, Giovanni Bussotti, Jia-Ming Chang, Paolo Di Tommaso, Ionas Erb, Jose Espinosa-Carrasco, Carsten Kemena & Cedric Notredame

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  1. Jean-Francois Taly
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Correspondence to Cedric Notredame.

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Taly, JF., Magis, C., Bussotti, G. et al. Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures. Nat Protoc 6, 1669–1682 (2011). https://doi.org/10.1038/nprot.2011.393

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