A Lagrangian relaxation approach for the multiple sequence alignment problem
نویسندگان
چکیده
منابع مشابه
A Lagrangian Relaxation Approach for the Multiple Sequence Alignment Problem
We present a branch-and-bound (bb) algorithm for the multiple sequence alignment problem (MSA), one of the most important problems in computational biology. The upper bound at each bb node is based on a Lagrangian relaxation of an integer linear programming formulation for MSA. Dualizing certain inequalities, the Lagrangian subproblem becomes a pairwise alignment problem, which can be solved ef...
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In contrast to proteins, many classes of functionally related RNA molecules show a rather weak sequence conservation but instead a fairly well conserved secondary structure. Hence it is clear, that any method that relates RNA sequences in form of (multiple) alignments should take structural features into account. Since multiple alignments are of great importance for subsequent data analysis, re...
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We introduce a new multiple sequence alignment method for protein sequences. We name our method HSA (Horizontal Sequence Alignment) for it horizontally slides a window on the protein sequences simultaneously. 2 HSA is superior to the existing methods that depend on the order of proteins since we consider all the proteins at once. Unlike most of the existing multiple alignment methods, HSA takes...
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ژورنال
عنوان ژورنال: Journal of Combinatorial Optimization
سال: 2008
ISSN: 1382-6905,1573-2886
DOI: 10.1007/s10878-008-9139-z