This Article 
   
 Share 
   
 Bibliographic References 
   
 Add to: 
 
Digg
Furl
Spurl
Blink
Simpy
Google
Del.icio.us
Y!MyWeb
 
 Search 
   
Study of the Paired Change Points in Bacterial Genes
PrePrint
ISSN: 1545-5963
It is known that nucleotide sequences are not totally homogeneous and this heterogeneity could not be due to random fluctuations only. Such heterogeneity poses a problem of making sequence segmentation into a set of homogeneous parts divided by the points called "change points". In this work we investigated a special case of change points – paired change points (PCP). We used a well-known property of coding sequences – triplet periodicity (TP). The sequences that we are especially interested in consist of three successive parts: the first and the last parts have similar TP while the middle part has different TP type. We aimed to find the genes with PCP and provide explanation for this phenomenon. We developed a mathematical method for the PCP detection based on the new measure of similarity between TP matrices. We investigated 66936 bacterial genes from 17 bacterial genomes and revealed 2700 genes with PCP and 6459 genes with single change point (SCP). We developed a mathematical approach to visualize the PCP cases. We suppose that PCP could be associated with double fusion or insertion events. The results of investigating the sequences with artificial insertions/fusions and distribution of TP inside the genome support the idea that the real number of genes formed by insertion/fusion events could be 5-7 times greater than the number of genes revealed in the present work.
Citation:
Eugene Korotkov, Maria Korotkova, "Study of the Paired Change Points in Bacterial Genes," IEEE/ACM Transactions on Computational Biology and Bioinformatics, 22 May 2014. IEEE computer Society Digital Library. IEEE Computer Society, <http://doi.ieeecomputersociety.org/10.1109/TCBB.2014.2321154>
Usage of this product signifies your acceptance of the Terms of Use.