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PMID: 3753762 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

Sequence landscapes.

Nucleic acids research ·Vol. 14 ·No. 1 ·1986-01-10 ·Pages 141-58

Clift B, Haussler D, McConnell R, Schneider TD, Stormo GD

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.

MeSH Terms
DNA, Viral/analysis Information Systems Repetitive Sequences, Nucleic Acid Software T-Phages/genetics Time Factors
Chemicals
DNA, Viral
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Clift B
Haussler D
McConnell R
Schneider T D
Stormo G D
References (13)
13 references, click to expand
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/14.1.141
Published
1986-01-10
Pages
141-58
Language
English
Region
England
NLM ID
0411011
PMCID
PMC339363
Subset
IM
Grants
NIGMS NIH HHS · GM28755 · United States
NCRR NIH HHS · RR01538 · United States
External Links
PubMed source DOI: 10.1093/nar/14.1.141 PMC Full Text View journal details
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