Noise‐reduction filtering for accurate detection of replication termini in bacterial genomes

Arakawa, Kazuharu; Saito, Rintaro; Tomita, Masaru

doi:10.1016/j.febslet.2006.12.021

Cited by 13 publications

(15 citation statements)

References 42 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The power spectrum PS ( k ) of F ( k ) was further defined as

PS false(k false) = | F false(k false) |^{2}, k = 0, 1, 2, \dots, N - 1

at each frequency k . In this power spectrum, GC skew shows the greatest contributing component at 1-Hz frequency, corresponding to the two replichores shifting between two regions of opposite polarity as in a sine curve (Arakawa et al 2007). The Math:FFT module of Perl (http://search.cpan.org/~rkobes/Math-FFT-1.28/FFT.pm) was used for FFT calculation.…”

Section: Methodsmentioning

confidence: 99%

The GC Skew Index: A Measure of Genomic Compositional Asymmetry and the Degree of Replicational Selection

Arakawa

Tomita

2007

Evol Bioinform Online

Self Cite

View full text Add to dashboard Cite

Circular bacterial chromosomes have highly polarized nucleotide composition in the two replichores, and this genomic strand asymmetry can be visualized using GC skew graphs. Here we propose and discuss the GC skew index (GCSI) for the quantification of genomic compositional skew, which combines a normalized measure of fast Fourier transform to capture the shape of the skew graph and Euclidean distance between the two vertices in a cumulative skew graph to represent the degree of skew. We calculated GCSI for all available bacterial genomes, and GCSI correlated well with the visibility of GC skew. This novel index is useful for estimating confidence levels for the prediction of replication origin and terminus by methods based on GC skew and for measuring the strength of replicational selection in a genome.

show abstract

“…The power spectrum PS ( k ) of F ( k ) was further defined as

PS false(k false) = | F false(k false) |^{2}, k = 0, 1, 2, \dots, N - 1

Section: Methodsmentioning

confidence: 99%

The GC Skew Index: A Measure of Genomic Compositional Asymmetry and the Degree of Replicational Selection

Arakawa

Tomita

2007

Evol Bioinform Online

Self Cite

View full text Add to dashboard Cite

show abstract

“…By using the available sequence information it was observed that the change in the GC skew points towards the dif chromosome dimer resolution site as the main fork fusion site, rather than any of the ter sites [52,53,54,55]. Differences in the types and rates of single base mutations in the leading and the lagging strand are thought to result in asymmetric replication-related mutation pressures, leading to the accumulation of G over C in the leading strand [55,56,57].…”

Section: The Location Of Fork Fusion Eventsmentioning

confidence: 99%

Replication Termination: Containing Fork Fusion-Mediated Pathologies in Escherichia coli

Dimude

Midgley-Smith

Stein

et al. 2016

Genes

View full text Add to dashboard Cite

Duplication of bacterial chromosomes is initiated via the assembly of two replication forks at a single defined origin. Forks proceed bi-directionally until they fuse in a specialised termination area opposite the origin. This area is flanked by polar replication fork pause sites that allow forks to enter but not to leave. The precise function of this replication fork trap has remained enigmatic, as no obvious phenotypes have been associated with its inactivation. However, the fork trap becomes a serious problem to cells if the second fork is stalled at an impediment, as replication cannot be completed, suggesting that a significant evolutionary advantage for maintaining this chromosomal arrangement must exist. Recently, we demonstrated that head-on fusion of replication forks can trigger over-replication of the chromosome. This over-replication is normally prevented by a number of proteins including RecG helicase and 3’ exonucleases. However, even in the absence of these proteins it can be safely contained within the replication fork trap, highlighting that multiple systems might be involved in coordinating replication fork fusions. Here, we discuss whether considering the problems associated with head-on replication fork fusion events helps us to better understand the important role of the replication fork trap in cellular metabolism.

show abstract

“…In eubacteria, the replication-related strand asymmetry results in two replichores of nearly equal lengths (note that replichores are not exactly symmetrical in many bacteria, especially in the phylum Firmicutes) but with opposite polarity. GC skew graphs in these species therefore resemble the graph of a discrete sine curve, a graph composed of Y = -1 for t 0 ~ (t 1 - t 0 )/2 and Y = 1 for (t 1 - t 0 )/2 ~ t 1 , and this “shape” of the GC skew graph can be assessed by observing the strength of the 1 Hz signal of its Fourier transformation [68]. Fourier transformation mathematically decomposes a given signal into a set of constituent frequencies, and the most simple frequency component of 1 Hz corresponds to a sine curve spanning all across the given signal duration.…”

Section: Measures Of Strand Biasmentioning

confidence: 99%

“…Numerous methods have been proposed for the analysis of compositional asymmetries, including multivariate statistics [31, 67] and signal processing methods based on Fourier [68] and wavelet transformations [50, 69] and wavelet-based multifractal analysis [70] (see [61] for comprehensive review). The key to these analyses is the quantitative measurement of the strength of strand bias.…”

Section: Introductionmentioning

confidence: 99%

Measures of Compositional Strand Bias Related to Replication Machinery and its Applications

Arakawa

Tomita²

2012

Self Cite

View full text Add to dashboard Cite

The compositional asymmetry of complementary bases in nucleotide sequences implies the existence of a mutational or selectional bias in the two strands of the DNA duplex, which is commonly shaped by strand-specific mechanisms in transcription or replication. Such strand bias in genomes, frequently visualized by GC skew graphs, is used for the computational prediction of transcription start sites and replication origins, as well as for comparative evolutionary genomics studies. The use of measures of compositional strand bias in order to quantify the degree of strand asymmetry is crucial, as it is the basis for determining the applicability of compositional analysis and comparing the strength of the mutational bias in different biological machineries in various species. Here, we review the measures of strand bias that have been proposed to date, including the ∆GC skew, the B1 index, the predictability score of linear discriminant analysis for gene orientation, the signal-to-noise ratio of the oligonucleotide bias, and the GC skew index. These measures have been predominantly designed for and applied to the analysis of replication-related mutational processes in prokaryotes, but we also give research examples in eukaryotes.

show abstract

Noise‐reduction filtering for accurate detection of replication termini in bacterial genomes

Cited by 13 publications

References 42 publications

The GC Skew Index: A Measure of Genomic Compositional Asymmetry and the Degree of Replicational Selection

The GC Skew Index: A Measure of Genomic Compositional Asymmetry and the Degree of Replicational Selection

Replication Termination: Containing Fork Fusion-Mediated Pathologies in Escherichia coli

Measures of Compositional Strand Bias Related to Replication Machinery and its Applications

Contact Info

Product

Resources

About