TY - JOUR
T1 - Noise-reduction filtering for accurate detection of replication termini in bacterial genomes
AU - Arakawa, Kazuharu
AU - Saito, Rintaro
AU - Tomita, Masaru
N1 - Funding Information:
We thank Haruo Suzuki for technical advice on the use of CAI to detect putative horizontally transferred genes, and the members of MGSP at the Institute for Advanced Biosciences, Keio University, for critical discussions. We are also grateful for the expert secretarial assistance of Sachiko Yasuda. This research was supported by the Japan Society for the Promotion of Science (JSPS).
PY - 2007/1/23
Y1 - 2007/1/23
N2 - 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.
AB - 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.
KW - Fast Fourier transform
KW - GC skew
KW - Horizontally transferred genes
KW - Origin of replication
KW - Polarization of chromosome
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U2 - 10.1016/j.febslet.2006.12.021
DO - 10.1016/j.febslet.2006.12.021
M3 - Article
C2 - 17188685
AN - SCOPUS:33846200467
SN - 0014-5793
VL - 581
SP - 253
EP - 258
JO - FEBS Letters
JF - FEBS Letters
IS - 2
ER -