Sequence landscapes

B. Clift, D. Haussler, R. Mcconnell, T. D. Schneider, G. D. Stormo

Research output: Contribution to journalArticlepeer-review

41 Scopus citations

Abstract

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.

Original languageEnglish
Pages (from-to)141-158
Number of pages18
JournalNucleic acids research
Volume14
Issue number1
DOIs
StatePublished - Jan 10 1986

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