National University of Nuclear Investigations (MIFI), Moscow 115409, Russia.
Genomics Proteomics Bioinformatics. 2011 Oct;9(4-5):158-70. doi: 10.1016/S1672-0229(11)60019-3.
The concept of the phase shift of triplet periodicity (TP) was used for searching potential DNA insertions in genes from 17 bacterial genomes. A mathematical algorithm for detection of these insertions has been developed. This approach can detect potential insertions and deletions with lengths that are not multiples of three bases, especially insertions of relatively large DNA fragments (>100 bases). New similarity measure between triplet matrixes was employed to improve the sensitivity for detecting the TP phase shift. Sequences of 17,220 bacterial genes with each consisting of more than 1,200 bases were analyzed, and the presence of a TP phase shift has been shown in ∼16% of analysed genes (2,809 genes), which is about 4 times more than that detected in our previous work. We propose that shifts of the TP phase may indicate the shifts of reading frame in genes after insertions of the DNA fragments with lengths that are not multiples of three bases. A relationship between the phase shifts of TP and the frame shifts in genes is discussed.
利用三重周期（TP）相移的概念，我们在 17 个细菌基因组的基因中搜索潜在的 DNA 插入。为此，我们开发了一种用于检测这些插入的数学算法。该方法可以检测长度不是三个碱基倍数的潜在插入和缺失，尤其是相对较大的 DNA 片段（>100 个碱基）的插入。我们采用了新的三矩阵相似性度量方法来提高检测 TP 相移的灵敏度。分析了由 17220 个细菌基因组成的序列，每个序列都超过 1200 个碱基，结果表明约 16%（2809 个）的分析基因中存在 TP 相移，这比我们之前的研究检测到的数量增加了约 4 倍。我们认为，在插入长度不是三个碱基倍数的 DNA 片段后，TP 相移可能会导致基因阅读框的移位。讨论了 TP 相移与基因框架移位之间的关系。
