Three-base periodicity patterns and self-similarity in whole bacterial chromosomes

López‐Villaseñor, Imelda; José, Marco V.; Sánchez, Jesús R.

doi:10.1016/j.bbrc.2004.10.053

Cited by 15 publications

(16 citation statements)

References 17 publications

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“…Using annotation tracks, we confirmed that these sequences correlated very closely to protein coding regions. This is a basic signature of protein coding regions already documented in the literature [3-5]. The basic 3-mer frequency pattern visualized in Skittle has previously been useful for identifying exons and even indicating reading frame and direction of the exon [7].…”

Section: Resultsmentioning

confidence: 93%

“…Some of these patterns have been associated with known genetic factors. For example, a 3-base-pair repeating pattern has been found to be characteristic of exonic regions [4,5], and a 10-11-base-pair motif has been found to be characteristic of DNA prone to supercoiling [6]. We expect a large part of future genomic analyses to involve the recognition and mapping of these and other multi-dimensional patterns.…”

Section: Introductionmentioning

confidence: 99%

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Skittle: A 2-Dimensional Genome Visualization Tool

Seaman¹,

Sanford

2009

BMC Bioinformatics

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BackgroundIt is increasingly evident that there are multiple and overlapping patterns within the genome, and that these patterns contain different types of information - regarding both genome function and genome history. In order to discover additional genomic patterns which may have biological significance, novel strategies are required. To partially address this need, we introduce a new data visualization tool entitled Skittle.ResultsThis program first creates a 2-dimensional nucleotide display by assigning four colors to the four nucleotides, and then text-wraps to a user adjustable width. This nucleotide display is accompanied by a "repeat map" which comprehensively displays all local repeating units, based upon analysis of all possible local alignments. Skittle includes a smooth-zooming interface which allows the user to analyze genomic patterns at any scale.Skittle is especially useful in identifying and analyzing tandem repeats, including repeats not normally detectable by other methods. However, Skittle is also more generally useful for analysis of any genomic data, allowing users to correlate published annotations and observable visual patterns, and allowing for sequence and construct quality control.ConclusionsPreliminary observations using Skittle reveal intriguing genomic patterns not otherwise obvious, including structured variations inside tandem repeats. The striking visual patterns revealed by Skittle appear to be useful for hypothesis development, and have already led the authors to theorize that imperfect tandem repeats could act as information carriers, and may form tertiary structures within the interphase nucleus.

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Section: Resultsmentioning

confidence: 93%

Section: Introductionmentioning

confidence: 99%

Skittle: A 2-Dimensional Genome Visualization Tool

Seaman¹,

Sanford

2009

BMC Bioinformatics

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“…The codon order of genes is associated with mRNA secondary structure, encoded protein, DNA-protein interaction and other biological characteristics. In addition, the triplets in mRNA that are spaced in 3n distances can produce three-base periodicity [13], indicating that certain codon combinations probably result in the periodicity in exons [14]. Therefore, the order of codons in the native sequences determines their differences from the codon-shuffled sequences, and also contributes to differences in neighbouring effects among substitution categories.…”

Section: Discussionmentioning

confidence: 99%

“…Later research suggested that the periodicity in exons arose due to the bias of codon usage frequencies [12]. Other studies proposed that three-base periodicity was determined by a preference for triplets that are separated by 3, 6 and 9 nucleotides (3n distances) in mRNA [13,14]. As a gene monitoring approach, three-base periodicity can be used to predict protein coding sequences [15].…”

Section: Introductionmentioning

confidence: 99%

Patterns of nucleotides that flank substitutions in human orthologous genes

Zhang

Huang

et al. 2010

BMC Genomics

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BackgroundSequence context is an important aspect of base mutagenesis, and three-base periodicity is an intrinsic property of coding sequences. However, how three-base periodicity is influenced in the vicinity of substitutions is still unclear. The effect of context on mutagenesis should be revealed in the usage of nucleotides that flank substitutions. Relative entropy (also known as Kullback-Leibler divergence) is useful for finding unusual patterns in biological sequences.ResultsUsing relative entropy, we visualized the periodic patterns in the context of substitutions in human orthologous genes. Neighbouring patterns differed both among substitution categories and within a category that occurred at three codon positions. Transition tended to occur in periodic sequences relative to transversion. Periodic signals were stronger in a set of flanking sequences of substitutions that occurred at the third-codon positions than in those that occurred at the first- or second-codon positions. To determine how the three-base periodicity was affected near the substitution sites, we fitted a sine model to the values of the relative entropy. A sine of period equal to 3 is a good approximation for the three-base periodicity at sites not in close vicinity to some substitutions. These periods were interrupted near the substitution site and then reappeared away from substitutions. A comparative analysis between the native and codon-shuffled datasets suggested that the codon usage frequency was not the sole origin of the three-base periodicity, implying that the native order of codons also played an important role in this periodicity. Synonymous codon shuffling revealed that synonymous codon usage bias was one of the factors responsible for the observed three-base periodicity.ConclusionsOur results offer an efficient way to illustrate unusual periodic patterns in the context of substitutions and provide further insight into the origin of three-base periodicity. This periodicity is a result of the native codon order in the reading frame. The length of the period equal to 3 is caused by the usage bias of nucleotides in synonymous codons. The periodic features in nucleotides surrounding substitutions aid in further understanding genetic variation and nucleotide mutagenesis.

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“…Nosúltimos anos essa característica nas CDSs tem sido analisada para explicar sua causa [25,43,53,56,64] e quantificá-la [20,47]. Na literatura, esta periodicidadeé chamada de periodicidade de três bases (TBP, three-base periodicity), tendo sido observada de maneira semelhante para di-nucleotídeos em cromossomos de bactérias [35].…”

Section: Periodicidade Nas Cdssunclassified

Identificação de regiões codificantes de proteína através da transformada modificada de Morlet

Chalco¹

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Three-base periodicity patterns and self-similarity in whole bacterial chromosomes

Cited by 15 publications

References 17 publications

Skittle: A 2-Dimensional Genome Visualization Tool

Skittle: A 2-Dimensional Genome Visualization Tool

Patterns of nucleotides that flank substitutions in human orthologous genes

Identificação de regiões codificantes de proteína através da transformada modificada de Morlet

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