Building multiple alignment using iterative dynamic improvement of the initial motif alignment

We studied the quality of restoration of true alignment columns depending on an initial alignment with a dynamic iterative improvement [1]. Even with weak similarity of the aligned sequences, iterative improvement of initial multiple alignment built using the motif method [2] 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).