Abstract
Elucidation of interrelationship among sequence, structure, function, and evolution of a family of genes or gene products is a central theme of modern molecular biology. Multiple sequence alignment is a powerful tool for such many-sided studies. We have developed a new strategy called "doubly nested randomized iterative method" to tackle this computationally hard problem. When tested upon structural alignments as references, our method was proven to perform significantly better than currently most popular methods. Our method will be applicable to a variety of problems, such as phylogenetic reconstruction, and prediction of functionally important regions and higher order structures of proteins.
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