Invited keynote: Prof. Cedric Notredame.
Multiple survival strategies to deal with the multiplication of multiple sequence alignment methods.
In this seminar I will introduce some of the latest developments in the field of multiple sequence alignment construction, including some of the work from my group. I will briefly review the main challenges and the latest work in the field, including ClustalO and the phylogeny aware aligners like SATe and how these aligners relate to consistency based methods like T-Coffee. I will also look at the complex relationship between multiple sequence alignment accuracy, structural modeling and phylogenetic tree reconstruction and introduce the notion of reliability index while reviewing some of the latest advances in this field, including the TCS (Transitive consistency score). I will show how this index can be used to both identify structurally correct positions in an alignment and evolutionary informative sites, thus suggesting more unity than initially thought between these two parameters. I will then introduce the structure based clustering method we recently developed to further test these hypothesis. I will finish with some consideration on the main challenges that need to be confronted for the accurate modeling of biological sequences relationship with a special attention on genomic and RNA sequences. All methods are available from www.tcoffee.org.
- TCS: a new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction. Chang JM, Di Tommaso P, Notredame C. Mol Biol Evol. 2014 Jun;31(6):1625-37. doi: 10.1093/molbev/msu117. Epub 2014 Apr 1.
- Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package. Kemena C, Bussotti G, Capriotti E, Marti-Renom MA, Notredame C. Bioinformatics. 2013 May 1;29(9):1112-9. doi: 10.1093/bioinformatics/btt096. Epub 2013 Feb 28.
- Alignathon: a competitive assessment of whole-genome alignment methods. Earl D, Nguyen N, Hickey G, Harris RS, Fitzgerald S, Beal K, Seledtsov I, Molodtsov V, Raney BJ, Clawson H, Kim J, Kemena C, Chang JM, Erb I, Poliakov A, Hou M, Herrero J, Kent WJ, Solovyev V, Darling AE, Ma J, Notredame C, Brudno M, Dubchak I, Haussler D, Paten B. Genome Res. 2014 Dec;24(12):2077-89. doi: 10.1101/gr.174920.114. Epub 2014 Oct 1.
- Epistasis as the primary factor in molecular evolution. Breen MS, Kemena C, Vlasov PK, Notredame C, Kondrashov FA. Nature. 2012 Oct 25;490(7421):535-8. doi: 10.1038/nature11510. Epub 2012 Oct 14.