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Literature DB >> 3753762

Sequence landscapes.

B Clift, D Haussler, R McConnell, T D Schneider, G 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.

Entities: Species

Mesh：

Substances：
DNA, Viral

Year: 1986 PMID： 3753762 PMCID： PMC339363 DOI： 10.1093/nar/14.1.141

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

13 in total

Sequence landscapes.

1. Computer analysis of nucleic acid regulatory sequences.

2. Recognition sequence of the dam methylase of Escherichia coli K12 and mode of cleavage of Dpn I endonuclease.

3. A design for computer nucleic-acid-sequence storage, retrieval, and manipulation.

4. Nucleotide sequence of bacteriophage G4 DNA.

5. Adsorption complex of filamentous fd virus.

6. The nucleotide sequence of bacteriophage phiX174.

7. Nucleotide sequence of bacteriophage fd DNA.

8. Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene.

9. Nucleotide sequence and genome organisation of filamentous bacteriophages fl and fd.

10. Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface.

1. Profile of David Haussler.

2. Excess information at bacteriophage T7 genomic promoters detected by a random cloning technique.

3. Similarity landscapes: a way to detect many structural and sequence motifs in both introns and exons.

4. TRedD--a database for tandem repeats over the edit distance.

5. Browsing repeats in genomes: Pygram and an application to non-coding region analysis.

6. HyDA-Vista: towards optimal guided selection of k-mer size for sequence assembly.

Review 7. No wisdom in the crowd: genome annotation in the era of big data - current status and future prospects.

8. Differentially Expressed Hepatic Genes Revealed by Transcriptomics in Pigs with Different Liver Lipid Contents.

9. ReRep: computational detection of repetitive sequences in genome survey sequences (GSS).

10. DNA sequences at a glance.