Building Multiple Alignment Using Iterative Dynamic Improvement of the Initial Motif Alignment

V. K. Nikolaev,¹ A. M. Leontovich,² V. A. Drachev,² and L. I. Brodsky^1,3

¹Gendalf Ltd., Moscow, Russia; E-mail: libro@cdrm.genebee.msu.su

²Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119899 Russia; fax: (7-095) 939-31-81; E-mail: libro@genebee.msu.su

³To whom correspondence should be addressed.

Submitted January 31, 1997; revision submitted March 13, 1997.

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We studied the quality of restoration of true alignment columns depending on an initial alignment with a dynamic iterative improvement (Hirosawa et al., 1995). Even with weak similarity of the aligned sequences, iterative improvement of initial multiple alignment built using the motif method (Brodsky et al., 1993) leads to an alignment close to the optimal. Moreover, it is important that the constructed alignment, by its "strong" positions (with good internal homology), is very similar to the "true" one for the given group of sequences. When verification was done, as a "true" one either a biologically correct alignment or one made using computer mutation of an "ancestral" alignment was taken. The iterative algorithm for dynamic improvement of motif alignment was incorporated into the program "Multiple Alignment" on the WWW server of the Belozersky Institute of Physico-Chemical Biology of Moscow State University (http://www.genebee.msu.su).

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KEY WORDS: alignment of sequences, motif alignment, dynamic programming, iterative method, WWW.

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