Compile of a complete map of local similarity for two biopolymers (DotHelix PROGRAM of the GenBee package)

Authors

  • A. M. Leontovich Coop 2 "ComBee" associated with Soviet-French-Italian Joint Venture "Interquadro" Moscow, USSR Author
  • L. I. Brodsky Coop 2 "ComBee" associated with Soviet-French-Italian Joint Venture "Interquadro" Moscow, USSR; A. N. Belozersky Interfaculty Laboratory of Molecular Biology and Bioorganic Chemistry, M. V. Lomonosov State University Moscow, USSR Author
  • A. E. Gorbalenya Institute of Poliomyelitis and Viral Encephalitides, Academy of Medical Sciences of the USSR Moscow Region, USSR Author

DOI:

https://doi.org/10.7124/bc.00029A

Abstract

A novel algorithm for generation of complete maps of local similarity for two biopolymers which is much faster than the similar Altschul-Erickson algorithm is described. This algorithm was implemented as the DotHelix program within the GenBee package. The algorithm effectiveness as compared to the Staden algorithm and the results obtained with the DotHelix program are illustrated by the comparison of the polyproteins of two strains of poliomyelitis virus type 3. The possible applications of the program are discussed in brief.

References

Staden R. An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences. Nucleic Acids Res. 1982;10(9):2951-61.

Altschul SF, Erickson BW. A nonlinear measure of subalignment similarity and its significance levels. Bull Math Biol. 1986;48(5-6):617-32.

Dayhoff MO, Barker WC, Hunt LT. Establishing homologies in protein sequences. Methods Enzymol. 1983;91:524-45.

Gorbalenia AE, Donchenko AP, Blinov VM. Possible common origin of poliovirus proteins responsible for different functions. Mol Gen Mikrobiol Virusol. 1986;(1):36-41.

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Published

1990-11-20

Issue

Vol. 6 No. 6 (1990)

Section

Biopolymers and Cell