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

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

Bacterial chromosomes are highly polarized in their nucleotide composition through mutational selection related to replication. Using compositional skews such as the GC skew, replication origin and terminus can be predicted in silico by observing the shift points. However, the genome sequence is affected by myriad functional requirements and selection on numerous subgenomic features, and elimination of this "noise" should lead to better predictions. Here, we present a noise-reduction approach that uses low-pass filtering through Fast Fourier transform coupled with cumulative skew graphs. It increases the prediction accuracy of the replication termini compared with previously documented methods based on genomic base composition.

Original languageEnglish
Pages (from-to)253-258
Number of pages6
JournalFEBS Letters
Volume581
Issue number2
DOIs
Publication statusPublished - 2007 Jan 23

Fingerprint

Bacterial Genomes
Noise abatement
Noise
Genes
Bacterial Chromosomes
Replication Origin
Base Composition
Fourier Analysis
Chromosomes
Chemical analysis
Computer Simulation
Fast Fourier transforms
Nucleotides
Genome

Keywords

  • Fast Fourier transform
  • GC skew
  • Horizontally transferred genes
  • Origin of replication
  • Polarization of chromosome

ASJC Scopus subject areas

  • Biochemistry
  • Biophysics
  • Molecular Biology

Cite this

Noise-reduction filtering for accurate detection of replication termini in bacterial genomes. / Arakawa, Kazuharu; Saito, Rintaro; Tomita, Masaru.

In: FEBS Letters, Vol. 581, No. 2, 23.01.2007, p. 253-258.

Research output: Contribution to journalArticle

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