The aqcelerated algorithm of dot homology matrix calculation

Authors

  • V. A. Shepelev Institute of Molecular Genetics, Academy of Sciences of the USSR Moscow, USSR Author

DOI:

https://doi.org/10.7124/bc.0002AC

Abstract

The method for analysis of homologous regions using dot matrices consists in finding and graphical representation of words common for two sequences on a rectangular matrix, i. e. subsequencies of length W with at least M coinciding letters. The algorithm: is suggested for accelerated calculation of dot matrices with the different filtration parameters. The time saving equals 6.8 times for parallel calculation of four windows.

References

Gibbs AJ, McIntyre GA. The diagram, a method for comparing sequences. Its use with amino acid and nucleotide sequences. Eur J Biochem. 1970;16(1):1-11.

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

Golovanov EI, Shepelev VA, Aleksandrov AA. Software system for the study of nucleotide sequences on microcomputers Iskra-226. Theor. research and molecular data base on biology and genetics. Novosibirsk, 1986:59-60.

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Published

1991-01-20

Issue

Vol. 7 No. 1 (1991)

Section

Biopolymers and Cell