Extension of the scope of Multiple Sequence Alignment Methods

Extension of the scope of Multiple Sequence Alignment Methods

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T-Coffee is a popular multiple sequence alignment method built around an original consistency based algorithm. Its main characteristic is the ability to combine heterogeneous types of information such as sequences, structures and annotation. With more than 1000 citations, T-Coffee is one of the most widely used Multiple Sequence Alignment Package. Its design makes it possible to use it either as an alignment package or as an alignment compiler. Our current goal is to extend the scope of T-Coffee in order to multiply compare a wider range of biological elements, ranging from genomes to short RNA sequences, and including more abstract data-structures like gene structures, metabolic pathways and interaction networks and the analysis of copy number variants. Such extension involve designing novel scoring function and optimization algorithms as well as collections of appropriate benchmarks.

All these projects are made in collaboration with Des Higgins (University College of Dublin) and Knut Reinhart (Berlin Free University).