Arakawa Kazuharu, Saito Rintaro, Tomita Masaru
Institute for Advanced Biosciences, Keio University, Fujisawa 252-8520, Japan.
FEBS Lett. 2007 Jan 23;581(2):253-8. doi: 10.1016/j.febslet.2006.12.021. Epub 2006 Dec 18.
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.
细菌染色体在核苷酸组成上通过与复制相关的突变选择而高度极化。利用诸如GC偏斜等组成偏斜，通过观察转移点可以在计算机上预测复制起点和终点。然而，基因组序列受到众多功能需求和对众多亚基因组特征的选择的影响，消除这种“噪声”应该会带来更好的预测。在这里，我们提出了一种降噪方法，该方法通过快速傅里叶变换结合累积偏斜图进行低通滤波。与之前基于基因组碱基组成的文献方法相比，它提高了复制终点的预测准确性。
