Sequence landscapes
- 10 January 1986
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 14 (1) , 141-158
- https://doi.org/10.1093/nar/14.1.141
Abstract
We describe a method for 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 bacteriophage T7, the DAWG 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.Keywords
This publication has 13 references indexed in Scilit:
- The nucleotide sequence of bacteriophage φX174Published by Elsevier ,2004
- Filamentous Fusion Phage: Novel Expression Vectors That Display Cloned Antigens on the Virion SurfaceScience, 1985
- A design for computer nucleic-acid-sequence storage, retrieval, and manipulationNucleic Acids Research, 1982
- Nucleotide sequence and genome organisation of filamentous bacteriophages f1 and fdGene, 1981
- Adsorption complex of filamentous fd virusJournal of Molecular Biology, 1981
- Recognition sequence of the dam methylase of Escherichia coli K12 and mode of cleavage of Dpn I endonuclease.Journal of Biological Chemistry, 1979
- Nucleotide sequence of bacteriophage G4 DNANature, 1978
- Nucleotide sequence of bacteriophage fd DNANucleic Acids Research, 1978
- Computer analysis of nucleic acid regulatory sequences.Proceedings of the National Academy of Sciences, 1977
- Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase geneNature, 1976