QOMA: quasi-optimal multiple alignment of protein sequences

QOMA: quasi-optimal multiple alignment of protein sequences

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Article ID: iaor2009348
Country: United Kingdom
Volume: 23
Start Page Number: 162
End Page Number: 168
Publication Date: Jan 2007
Journal: Bioinformatics
Authors: ,
Keywords: graphs, heuristics
Abstract:

We consider the problem of multiple alignment of protein sequences with the goal of achieving a large SP (Sum-of-Pairs) score. We introduce a new graph-based method. We name our method QOMA (Quasi-Optimal Multiple Alignment). QOMA starts with an initial alignment. It represents this alignment using a K-partite graph. It then improves the SP score of the initial alignment through local optimizations within a window that moves greedily on the alignment. QOMA uses two parameters to permit flexibility in time/accuracy trade off: (1) the size of the window for local optimization, (2) the sparsity of the K-partite graph.

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