Efficient Methods for Multiple Sequence Alignment with Guaranteed Error Bounds
Keywords and Synonyms
Multiple string alignment; Multiple global alignment
Multiple sequence alignment is an important problem in computational biology. Applications include finding highly conserved subregions in a given set of biological sequences and inferring the evolutionary history of a set of taxa from their associated biological sequences (e. g., see ). There are a number of measures proposed for evaluating the goodness of a multiple alignment, but prior to this work, no efficient methods are known for computing the optimal alignment for any of these measures. The work of Gusfield  gives two computationally efficient multiple alignment approximation algorithms for two of the measures with approximation ratio of less than 2. For one of the measures, they also derived a randomized algorithm, which is much faster and with high probability, reports a multiple alignment with small error bounds. To the best knowledge of the entry authors, this work is...
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