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Nucleic Acids Research, 1986, Vol. 14, No. 1 141-158
© 1986

Articles

Sequence landscapes

B. Clift, D. Haussler, R. McConnell, T.D. Schneider1 and G.D. Stormo1

Department of Mathematics and Computer Science, University of Denver Denver, CO 80208, USA 1Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, CO 80309, USA

Received July 16, 1985. We describe a method tor representing the structure of repeating sequences in nucleic-acids, proteins and other texts. A portion of the sequence is presented at the bottom of a CRT screen. Above the sequence is its landscape, which looks like a mountain range. Each mountain corresponds to a subsequence of the sequence. At the peak of every mountain is written the number of times that the subsequence appears. A data structure called a DAWG, which can be built in time proportional to the length of the sequence, is used to construct the landscape. For the 40 thousand bases of bacterlophage T7, the DAWQ can be built in 30 seconds. The time to display any portion of the landscape is less than a second. Using sequence landscapes, one can quickly locate significant repeats.


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