Search for Dispersed Repeats in Bacterial Genomes Using an Iterative Procedure.

We have developed a de novo method for the identification of dispersed repeats based on the use of random position-weight matrices (PWMs) and an iterative procedure (IP). The created algorithm (IP method) allows detection of dispersed repeats for which the average number of substitutions between any two repeats per nucleotide () is less than or equal to 1.5.

Multiple Alignment of Promoter Sequences from the L. Genome.

In this study, we developed a new mathematical method for performing multiple alignment of highly divergent sequences (MAHDS), i.e., sequences that have on average more than 2.

Study of the Paired Change Points in Bacterial Genes.

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).

Study of triplet periodicity differences inside and between genomes.

Triplet periodicity (TP) is a distinctive feature of the protein coding sequences of both prokaryotic and eukaryotic genomes. In this work, we explored the TP difference inside and between 45 prokaryotic genomes. We constructed two hypotheses of TP distribution on a set of coding sequences and generated artificial datasets that correspond to the hypotheses.

Comparative analysis of periodicity search methods in DNA sequences.

To determine the periodicity of a DNA sequence, different spectral approaches are applied (discrete Fourier transform (DFT), autocorrelation (CORR), information decomposition (ID), hybrid method (HYB), concept of spectral envelope for spectral analysis (SE), normalized autocorrelation (CORR_N) and profile analysis (PA). In this work, we investigated the possibility of finding the true period length, by depending on the average number of accumulated changes in DNA bases (PM) for the methods stated above. The results show that for periods with short length (≤4 b.

Detection change points of triplet periodicity of gene.

The triplet periodicity (TP) is a distinguished property of protein coding sequences. There are complex genes with more than one TP type along their sequence. We say that these genes contain a triplet periodicity change point.