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Tuesday, February 24, 2009
12:00 PM - 1:30 PM
CNLS Conference Room (TA-3, Bldg 1690)


Multiple Sequence Alignment - DIALIGN Approach: Basic Concepts and Recent Developments

Burkhard Morgenstern
University of Goettingen, Institute of Microbiology and Genetics

Multiple Sequence Alignment (MSA) is a fundamental step in nucleic acid and protein sequence analysis. Algorithms for MSA are therefore a central field of research in bioinformatics. Traditional MSA methods use either global or local algorithms. By contrast, the DIALIGN approach to MSA tries to combine global and local alignment aspects. Multiple alignments are constructed based on pairwise local sequence similarities. During the last years, various optimization algorithms have been applied to the resulting optimization problem. The latest release of the program, DIALIGN-TX combines a greedy strategy used in previous versions of the program with a more traditional progressive algorithm for MSA.

Another recent development was the introduction of anchored alignments where the program is forced to align certain user-defined regions of the input sequences. This option can be used to speed up the program, but it can also be used to obtain alignments that are biologically more meaningful than alignments produced by the default version of the program.

Host: Ming Zhang, T-6