Biopolym. Cell. 1991; 7(1):14-22.
http://dx.doi.org/10.7124/bc.000049
A novel method of multiple sequence alighment of biopolymers (program H-Align of the GenBee package)
1Brodsky L. I., 2Drachev A. L., 2Leontovich A. M.
  1. Coop 2 "ComBee" associated with Soviet-French-Italian Joint Venture "Interquadro"
    Moscow, USSR
  2. A. N. Belozersky Interfaculty Laboratory of Molecular Biology and Bioorganic Chemistry,
    M. V. Lomonosov State University
    Moscow, USSR

Abstract

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.
Full text: (PDF, in Russian)

References

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