PMID: 3753762Jan 10, 1986Paper

Sequence landscapes

Nucleic Acids Research
B CliftG D Stormo

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.

References

Oct 1, 1977·Proceedings of the National Academy of Sciences of the United States of America·L J KornM N Wegman
Nov 16, 1978·Nature·G N GodsonJ C Fiddes
Oct 25, 1978·Journal of Molecular Biology·F SangerM Smith
Dec 1, 1978·Nucleic Acids Research·E BeckM Takanami
Jan 11, 1984·Nucleic Acids Research·T D SchneiderL Gold
Jun 5, 1983·Journal of Molecular Biology·J J Dunn, F W Studier
Mar 15, 1981·Journal of Molecular Biology·C W GrayD A Marvin
May 11, 1982·Nucleic Acids Research·T D SchneiderL Gold

❮ Previous
Next ❯

Citations

Jul 15, 1999·Computers & Chemistry·M Crochemore, R Vérin
Sep 19, 2008·Proceedings of the National Academy of Sciences of the United States of America·Philip Downey
Aug 26, 2003·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Alberto ApostolicoStefano Lonardi
Jul 22, 1998·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·A BrazmaD Gilbert
Oct 17, 1998·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·M F Sagot, E W Myers
Jul 14, 2010·Database : the Journal of Biological Databases and Curation·Dina Sokol, Firat Atagun
Oct 28, 2006·BMC Bioinformatics·Patrick DurandJacques Nicolas
Sep 11, 2008·BMC Bioinformatics·Thomas D OttoWim M Degrave
Nov 28, 2013·PloS One·Armando J PinhoPaulo J S G Ferreira
Jan 7, 2015·BMC Genomics·Basir ShariatChristina Boucher
Apr 9, 2016·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Sharma V ThankachanSrinivas Aluru
May 29, 2018·Microbial Biotechnology·Antoine DanchinJean-Daniel Zucker

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
A von Haeseler, M Schöniger
Computer Applications in the Biosciences : CABIOS
G M LandauR Nussinov
© 2021 Meta ULC. All rights reserved