This course is dedicated to multiple sequence alignments. We will first describe the scope of this important modeling technique and analyze in details the most common algorithm. We will then see some of the important factors that affect the usefulness of these models. The second lecture will present T-Coffee a software developed in my lab that can be used to either align sequences, structures, or even to combine multiple structural alignments. In the afternoon we will see how T-Coffee can be used in order to generate highly accurate multiple sequence alignments of proteins, DNA and RNA.

1. Durbin, R., et al., Biological Sequence Analysis. 1998, Cambridge: Cambridge University Press.

2. Altschul, S.F., et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. nucleic acids res., 1997. 25(17): p. 2289-3402.

3. Notredame, C., D.G. Higgins, and J. Heringa, T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol, 2000. 302(1): p. 205-17.

4. Wallace, I.M., et al., M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res, 2006. 34(6): p. 1692-9.

5. Wilm, A., D.G. Higgins, and C. Notredame, R-Coffee: a method for multiple alignment of non-coding RNA. Nucleic Acids Res, 2008. 36(9): p. e52.

6. Bussoti, G., et al., BlastR: A new Tool for searching RNA in databases. Nucleic Acids Research, 2011.