Abstract
A new mathematical method is proposed for constructing multiple alignment of weakly similar amino acid or nucleotide sequences. The method uses a multiple alignment representation in the form of position-weight matrices (PWM) and global dynamic programming. An optimization procedure for PWM is developed with the aim of finding a multiple alignment with maximum statistical significance. The method allows to find multiple alignment of sequences with the number of nucleotide or amino acid substitutions more than 2.5. The developed approach is applied to obtain multiple alignment of promoter sequences of 600 DNA bases length.
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