An Approach for Searching Insertions in Bacterial Genes Leading to the Phase Shift of Triplet Periodicity  

作　　者：Maria A. Korotkova Nikolay A. Kudryashov Eugene V. Korotkov 

机构地区：[1]Centre of Bioengineering, Russian Academy of Sciences [2]National University of Nuclear Investigations (MIFI)

出　　处：《Genomics, Proteomics & Bioinformatics》2011年第4期158-170,共13页基因组蛋白质组与生物信息学报（英文版）

摘　　要：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.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.

关 键 词：triplet periodicity INSERTION gene sequence reading frame phase shift change-point problem 

分 类 号：Q93[生物学—微生物学]