bbc 2015
BBC2015_booklet
BBC2015_booklet
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BeNeLux Bioinformatics Conference – Antwerp, December 7-8 <strong>2015</strong><br />
Abstract ID: K2<br />
Keynote<br />
10th Benelux Bioinformatics Conference <strong>bbc</strong> <strong>2015</strong><br />
K2. MULTIPLE SURVIVAL STRATEGIES TO DEAL WITH THE<br />
MULTIPLICATION OF MULTIPLE SEQUENCE ALIGNMENT METHODS<br />
Cedric Notredame<br />
In this seminar I will introduce some of the latest developments in the field of multiple sequence alignment construction,<br />
including some of the work from my group. I will briefly review the main challenges and the latest work in the field,<br />
including ClustalO and the phylogeny aware aligners like SATe and how these aligners relate to consistency based<br />
methods like T-Coffee. I will also look at the complex relationship between multiple sequence alignment accuracy,<br />
structural modeling and phylogenetic tree reconstruction and introduce the notion of reliability index while reviewing<br />
some of the latest advances in this field, including the TCS (Transitive consistency score). I will show how this index can<br />
be used to both identify structurally correct positions in an alignment and evolutionary informative sites, thus suggesting<br />
more unity than initially thought between these two parameters. I will then introduce the structure based clustering<br />
method we recently developed to further test these hypothesis. I will finish with some consideration on the main<br />
challenges that need to be confronted for the accurate modeling of biological sequences relationship with a special<br />
attention on genomic and RNA sequences. All methods are available from www.tcoffee.org.<br />
REFERENCES<br />
TCS: a new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction. Chang<br />
JM, Di Tommaso P, Notredame C. Mol Biol Evol. 2014 Jun;31(6):1625-37. doi: 10.1093/molbev/msu117. Epub 2014 Apr 1.<br />
Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package. Kemena C, Bussotti G,<br />
Capriotti E, Marti-Renom MA, Notredame C. Bioinformatics. 2013 May 1;29(9):1112-9. doi: 10.1093/bioinformatics/btt096. Epub 2013 Feb 28.<br />
Alignathon: a competitive assessment of whole-genome alignment methods. Earl D, Nguyen N, Hickey G, Harris RS, Fitzgerald S, Beal K,<br />
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,<br />
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.<br />
Epub 2014 Oct 1.<br />
Epistasis as the primary factor in molecular evolution. Breen MS, Kemena C, Vlasov PK, Notredame C, Kondrashov FA. Nature. 2012 Oct<br />
25;490(7421):535-8. doi: 10.1038/nature11510. Epub 2012 Oct 14.<br />
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