Literature DB >> 8506142

Nucleotide, dinucleotide and trinucleotide frequencies explain patterns observed in chaos game representations of DNA sequences.

N Goldman1.   

Abstract

The chaos game representation (CGR) is a scatter plot derived from a DNA sequence, with each point of the plot corresponding to one base of the sequence. If the DNA sequence were a random collection of bases, the CGR would be a uniformly filled square; conversely, any patterns visible in the CGR represent some pattern (information) in the DNA sequence. In this paper, patterns previously observed in a variety of DNA sequences are explained solely in terms of nucleotide, dinucleotide and trinucleotide frequencies.

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Year:  1993        PMID： 8506142      PMCID： PMC309551          DOI： 10.1093/nar/21.10.2487

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


  10 in total

1.  Mathematical characterization of Chaos Game Representation. New algorithms for nucleotide sequence analysis.

Authors:  C Dutta; J Das
Journal:  J Mol Biol       Date:  1992-12-05       Impact factor: 5.469

2.  Enzymatic synthesis of deoxyribonucleic acid. VIII. Frequencies of nearest neighbor base sequences in deoxyribonucleic acid.

Authors:  J JOSSE; A D KAISER; A KORNBERG
Journal:  J Biol Chem       Date:  1961-03       Impact factor: 5.157

3.  Chaos game representation of gene structure.

Authors:  H J Jeffrey
Journal:  Nucleic Acids Res       Date:  1990-04-25       Impact factor: 16.971

4.  A statistical analysis of nucleotide sequences of introns and exons in human genes.

Authors:  M Bulmer
Journal:  Mol Biol Evol       Date:  1987-07       Impact factor: 16.240

5.  The analysis of intron data and their use in the detection of short signals.

Authors:  P J Avery
Journal:  J Mol Evol       Date:  1987       Impact factor: 2.395

Review 6.  Codon catalog usage and the genome hypothesis.

Authors:  R Grantham; C Gautier; M Gouy; R Mercier; A Pavé
Journal:  Nucleic Acids Res       Date:  1980-01-11       Impact factor: 16.971

7.  DNA methylation and the frequency of CpG in animal DNA.

Authors:  A P Bird
Journal:  Nucleic Acids Res       Date:  1980-04-11       Impact factor: 16.971

8.  Chaos game representation of coding regions of human globin genes and alcohol dehydrogenase genes of phylogenetically divergent species.

Authors:  K A Hill; N J Schisler; S M Singh
Journal:  J Mol Evol       Date:  1992-09       Impact factor: 2.395

9.  A Markov analysis of DNA sequences.

Authors:  H Almagor
Journal:  J Theor Biol       Date:  1983-10-21       Impact factor: 2.691
  10 in total
  20 in total

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

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Journal:  J Mol Evol       Date:  2005-07-19       Impact factor: 2.395

Review 2.  Sequence analysis by iterated maps, a review.

Authors:  Jonas S Almeida
Journal:  Brief Bioinform       Date:  2013-10-25       Impact factor: 11.622

3.  Capturing whole-genome characteristics in short sequences using a naïve Bayesian classifier.

Authors:  R Sandberg; G Winberg; C I Bränden; A Kaske; I Ernberg; J Cöster
Journal:  Genome Res       Date:  2001-08       Impact factor: 9.043

4.  Using genomic signatures for HIV-1 sub-typing.

Authors:  Aridaman Pandit; Somdatta Sinha
Journal:  BMC Bioinformatics       Date:  2010-01-18       Impact factor: 3.169

5.  Resolving prokaryotic taxonomy without rRNA: longer oligonucleotide word lengths improve genome and metagenome taxonomic classification.

Authors:  Eric B Alsop; Jason Raymond
Journal:  PLoS One       Date:  2013-07-01       Impact factor: 3.240

6.  Chaos game representation for comparison of whole genomes.

Authors:  Jijoy Joseph; Roschen Sasikumar
Journal:  BMC Bioinformatics       Date:  2006-05-05       Impact factor: 3.169

7.  Computing distribution of scale independent motifs in biological sequences.

Authors:  Jonas S Almeida; Susana Vinga
Journal:  Algorithms Mol Biol       Date:  2006-10-18       Impact factor: 1.405

8.  TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences.

Authors:  Hanno Teeling; Jost Waldmann; Thierry Lombardot; Margarete Bauer; Frank Oliver Glöckner
Journal:  BMC Bioinformatics       Date:  2004-10-26       Impact factor: 3.169

9.  Universal sequence map (USM) of arbitrary discrete sequences.

Authors:  Jonas S Almeida; Susana Vinga
Journal:  BMC Bioinformatics       Date:  2002-02-05       Impact factor: 3.169

10.  A supervised learning approach for taxonomic classification of core-photosystem-II genes and transcripts in the marine environment.

Authors:  Shani Tzahor; Dikla Man-Aharonovich; Benjamin C Kirkup; Tali Yogev; Ilana Berman-Frank; Martin F Polz; Oded Béjà; Yael Mandel-Gutfreund
Journal:  BMC Genomics       Date:  2009-05-16       Impact factor: 3.969
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