A novel method of multiple sequence alighment of biopolymers (program H-Align of the GenBee package)
DOI:
https://doi.org/10.7124/bc.000049Abstract
Summary Generalization of the multiple alignment is central to the entire field of biological sequence analysis. The algorithm of alignment by program H-align incorporated in GenBee package is a result of development of the local similarity search principle. It has two stages: 1) generalization of all the conservative regions (they cannot be present in all the aligning sequences). 2) optimal arrangement of these regions using two criteria — maximization of the total power of the conservative regions and minimization of the total number of spaces. This algorithm has at least two advantages over traditional algorithms (such as Needleman-Wunsch's one) : no penalty for insertion / deletion; not subsequent pair aligning procedure. The efficiency of the algorithm is shown at model example.References
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