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Nucleic Acids Research, 1982, Vol. 10, No. 1 365-374
© 1982

Articles

Two-dimensional graphic analysis of DNA sequence homologies

Robert Harr1,2, Per Hagblom1 and Petter Gustafsso1

1Department of Microbiology, University of Umea S-901 87 Umea 2Department of Chalmers University of Technology Sven Hultins väg, S-412 96, Göteborg, Sweden

Received September 23, 1981. We describe a computer program designed to facilitate the pattern matching analysis of homologies between DNA sequences. It takes advantage of a two-dimensional plot in order to simplify the evaluation of significant structures inherited in the sequences. The program can be divided into three parts, i) algorithm for search of homologies, ii) twodimensional graphic display of the result, iii) further graphic treatment to enhance significant structures.

The power of the graphic display is presented by the following application of the program. We have conducted a search for direct repeats in the mouse immunoglobulin K-chain genes. Both the five J DNA sequences and other shorter repeats were found. We also found a longer stretch of homology that could indicate the presence of duplicated DNA in the J4, J5 region.


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