Genomic signature is preserved in short DNA fragments

Deschavanne, Patrick; Giron, Alain; Vilain, Joseph; Dufraigne, Christine; Fertil, Bernard

doi:10.1109/bibe.2000.889603

Cited by 35 publications

(31 citation statements)

References 19 publications

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“…Campbell et al (1999) compared genomic signatures of prokaryote, plasmid, and mitochondrial DNA. Deschavanne et al (2000) showed that word usage in short fragments of genomic DNA (as short as 1 kb) is similar to that of the whole genome, thus providing a strong support to the concept of genomic signature. Gentles and Karlin (2001) looked at the genomic signature of various eukaryotes.…”

Section: Introductionmentioning

confidence: 88%

“…Since 1995, genomic signatures have been studied from a variety of perspectives, as witnessed by Karlin et al (1997), Campbell et al (1999), Deschavanne et al (1999Deschavanne et al ( , 2000, Gentles and Karlin (2001), Sandberg et al (2001), Edwards et al (2002), and Hao et al (2000). Campbell et al (1999) compared genomic signatures of prokaryote, plasmid, and mitochondrial DNA.…”

Section: Introductionmentioning

confidence: 99%

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The spectrum of genomic signatures: from dinucleotides to chaos game representation

Wang

Hill

Singh

et al. 2005

Gene

104

102

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Section: Introductionmentioning

confidence: 88%

Section: Introductionmentioning

confidence: 99%

The spectrum of genomic signatures: from dinucleotides to chaos game representation

Wang

Hill

Singh

et al. 2005

Gene

104

102

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“…In [9] Oliver et al used entropy based on density within the CGR to compare genes. Deschavanne observed that the CGR images can be viewed as a type of signature of the associated structure [10]. The authors conclude that even short segments maintain the same characteristics as does the entire species from which they come.…”

Section: Cgr Overviewmentioning

confidence: 96%

Visualization of DNA/RNA Structure using Temporal CGRs

Dunham

Quick

Wang

et al. 2006

Sixth IEEE Symposium on BioInformatics and BioEngineering (BIBE'06)

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We present a new DNA/RNA sequence visualization technique, Temporal Chaos Game Representation (TCGR), which is an extension of Frequency Chaos Game Representation (FCGR). Unlike earlier CGR variants, TCGR illustrates the distribution of nucleotide sub-patterns at different positions within a sequence, and it can be applied to sets of sequences as well as individual sequences. TCGRs are suitable for short or long sequences. Preliminary experiments examining patterns of nucleotide occurrences in micro-RNA data illustrate not only the informative nature of the images, but clearly indicate the variability of distributions based on position, and the similarity and differences of distributions across various species.

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“…The latter method illustrates a DNA sequence in the form of a 2D image [23][24][25], based on the Chaos Game theory [26] [27]. The method (we mean the FCGR) encodes the oligomers frequency of apparition according to given color scale; where each frequency occupies www.ijacsa.thesai.org a precise emplacement in the representation area.…”

Section: Mapping the Dna Sequences: From Character Strings Towarmentioning

confidence: 99%

A Coding Technique Based on the Frequency Evolution Creates with a Time Frequency Analysis a New Genome's Landscape

Messaoudi¹,

Elloumi²,

Lachiri³

2014

IJACSA

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Abstract-In recent years, considerable effort has been devoted to study the biological data sets within the framework of the genomic signal processing field. However, the enormous amount of data deposited into public databases makes the search for useful information a difficult task. Effectively, the choice for a convenient analysis approach is not at all obvious at all. In this work, we provide a new way to map the genomes within the form of images. The mapping uses the Complex Morlet wavelet as analysis technique and the Frequency Chaos Game Signal (FCGS) as digital dataset. Before processing the wavelet analysis, we build the FCGS in such a way that we can follow the frequency evolution of nucleotides' occurrence along the genome. The time-frequency analysis of the FCGS signals constitutes a pertinent tool for exploring the DNA structures in the C.elegans genome-wide landscape.

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Genomic signature is preserved in short DNA fragments

Cited by 35 publications

References 19 publications

The spectrum of genomic signatures: from dinucleotides to chaos game representation

The spectrum of genomic signatures: from dinucleotides to chaos game representation

Visualization of DNA/RNA Structure using Temporal CGRs

A Coding Technique Based on the Frequency Evolution Creates with a Time Frequency Analysis a New Genome's Landscape

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