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Literature DB >> 2336393

Chaos game representation of gene structure.

Abstract

This paper presents a new method for representing DNA sequences. It permits the representation and investigation of patterns in sequences, visually revealing previously unknown structures. Based on a technique from chaotic dynamics, the method produces a picture of a gene sequence which displays both local and global patterns. The pictures have a complex structure which varies depending on the sequence. The method is termed Chaos Game Representation (CGR). CGR raises a new set of questions about the structure of DNA sequences, and is a new tool for investigating gene structure.

Mesh：

Substances：
DNA

Year: 1990 PMID： 2336393 PMCID： PMC330698 DOI： 10.1093/nar/18.8.2163

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

2 in total

1. Origin of eukaryotic introns: a hypothesis, based on codon distribution statistics in genes, and its implications.

Authors: P Senapathy
Journal: Proc Natl Acad Sci U S A Date: 1986-04 Impact factor: 11.205

2. Statistical method for predicting protein coding regions in nucleic acid sequences.

Authors: G Fichant; C Gautier
Journal: Comput Appl Biosci Date: 1987-11

2 in total

110 in total

Review 1. Horizontal gene transfer and bacterial diversity.

Authors: Chitra Dutta; Archana Pan
Journal: J Biosci Date: 2002-02 Impact factor: 1.826

2. Equal G and C contents in histone genes indicate selection pressures on mRNA secondary structure.

Authors: M A Huynen; D A Konings; P Hogeweg
Journal: J Mol Evol Date: 1992-04 Impact factor: 2.395

3. Measuring the coding potential of genomic sequences through a combination of triplet occurrence patterns and RNY preference.

Authors: Christoforos Nikolaou; Yannis Almirantis
Journal: J Mol Evol Date: 2004-09 Impact factor: 2.395

Review 4. Identification of replication origins in archaeal genomes based on the Z-curve method.

Authors: Ren Zhang; Chun-Ting Zhang
Journal: Archaea Date: 2005-05 Impact factor: 3.273

5. "Word" preference in the genomic text and genome evolution: different modes of n-tuplet usage in coding and noncoding sequences.

Authors: Christoforos Nikolaou; Yannis Almirantis
Journal: J Mol Evol Date: 2005-07-19 Impact factor: 2.395

6. Indications for acquisition of reductive dehalogenase genes through horizontal gene transfer by Dehalococcoides ethenogenes strain 195.

Authors: Christophe Regeard; Julien Maillard; Christine Dufraigne; Patrick Deschavanne; Christof Holliger
Journal: Appl Environ Microbiol Date: 2005-06 Impact factor: 4.792

Chaos game representation of gene structure.

1. Origin of eukaryotic introns: a hypothesis, based on codon distribution statistics in genes, and its implications.

2. Statistical method for predicting protein coding regions in nucleic acid sequences.

Review 1. Horizontal gene transfer and bacterial diversity.

2. Equal G and C contents in histone genes indicate selection pressures on mRNA secondary structure.

3. Measuring the coding potential of genomic sequences through a combination of triplet occurrence patterns and RNY preference.

Review 4. Identification of replication origins in archaeal genomes based on the Z-curve method.

5. "Word" preference in the genomic text and genome evolution: different modes of n-tuplet usage in coding and noncoding sequences.

6. Indications for acquisition of reductive dehalogenase genes through horizontal gene transfer by Dehalococcoides ethenogenes strain 195.

Review 7. New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing.

Review 8. Sequence analysis by iterated maps, a review.

9. Fractals in the nervous system: conceptual implications for theoretical neuroscience.

10. Integrated mapping, chromosomal sequencing and sequence analysis of Cryptosporidium parvum.