Study of Dispersed Repeats in the Cyanidioschyzon merolae Genome.

In this study, we applied the iterative procedure (IP) method to search for families of highly diverged dispersed repeats in the genome of Cyanidioschyzon merolae, which contains over 16 million bases. The algorithm included the construction of position weight matrices (PWMs) for repeat families and the identification of more dispersed repeats based on the PWMs using dynamic programming. The results showed that the C. merolae genome contained 20 repeat families comprising a total of 33,938 dispersed repeats, which is significantly more than has been previously found using other methods. The repeats varied in length from 108 to 600 bp (522.54 bp in average) and occupied more than 72% of the C. merolae genome, whereas previously identified repeats, including tandem repeats, have been shown to constitute only about 28%. The high genomic content of dispersed repeats and their location in the coding regions suggest a significant role in the regulation of the functional activity of the genome.

Detection of tandem repeats in the Capsicum annuum genome.

In this study, we modified the multiple alignment method based on the generation of random position weight matrices (RPWM) and used it to search for tandem repeats (TRs) in the Capsicum annuum genome. The application of the modified (m)RPWM method, which considers the correlation of adjusting nucleotides, resulted in the identification of 908,072 TR regions with repeat lengths from 2 to 200 bp in the C. annuum genome, where they occupied ~29%. The most common TRs were 2 and 3 bp long followed by those of 21, 4, and 15 bp. We performed clustering analysis of TRs with repeat lengths of 2 and 21 bp and created position-weight matrices (PWMs) for each group; these templates could be used to search for TRs of a given length in any nucleotide sequence. All detected TRs can be accessed through publicly available database (http : //victoria.biengi.ac.ru/capsicum_tr/). Comparison of mRPWM with other TR search methods such as Tandem Repeat Finder, T-REKS, and XSTREAM indicated that mRPWM could detect significantly more TRs at similar false discovery rates, indicating its superior performance. The developed mRPWM method can be successfully applied to the identification of highly divergent TRs, which is important for functional analysis of genomes and evolutionary studies.

Database of Potential Promoter Sequences in the Capsicum annuum Genome.

In this study, we used a mathematical method for the multiple alignment of highly divergent sequences (MAHDS) to create a database of potential promoter sequences (PPSs) in the Capsicum annuum genome. To search for PPSs, 20 statistically significant classes of sequences located in the range from -499 to +100 nucleotides near the annotated genes were calculated. For each class, a position-weight matrix (PWM) was computed and then used to identify PPSs in the C. annuum genome. In total, 825,136 PPSs were detected, with a false positive rate of 0.13%. The PPSs obtained with the MAHDS method were tested using TSSFinder, which detects transcription start sites. The databank of the found PPSs provides their coordinates in chromosomes, the alignment of each PPS with the PWM, and the level of statistical significance as a normal distribution argument, and can be used in genetic engineering and biotechnology.

Search for Highly Divergent Tandem Repeats in Amino Acid Sequences.

We report a Method to Search for Highly Divergent Tandem Repeats (MSHDTR) in protein sequences which considers pairwise correlations between adjacent residues. MSHDTR was compared with some previously developed methods for searching for tandem repeats (TRs) in amino acid sequences, such as T-REKS and XSTREAM, which focus on the identification of TRs with significant sequence similarity, whereas MSHDTR detects repeats that significantly diverged during evolution, accumulating deletions, insertions, and substitutions. The application of MSHDTR to a search of the Swiss-Prot databank revealed over 15 thousand TR-containing amino acid sequences that were difficult to find using the other methods. Among the detected TRs, the most representative were those with consensus lengths of two and seven residues; these TRs were subjected to cluster analysis and the classes of patterns were identified. All TRs detected in this study have been combined into a databank accessible over the WWW.

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. The aim of the work is to find all genes that contain TP change point and attempt to compare the positions of change point in genes with known biological data. We have developed a mathematical method to identify triplet periodicity changes along a sequence. We have found 311,221 genes with the TP change point in the KEGG/Genes database (version 48). It is about 8% from the total database volume (4013150). We showed that the repetitive sequences are not the only cause of such events. We suppose that the TP change point may indicate a fusion of genes or domains. We performed BLAST analysis to find potential ancestral genes for the parts of genes with TP change point. As a result we found that in 131323 cases sequences with TP change point have proper similarities for one or both parts. The relationship between TP change point and the fusion events in genes is discussed. The program realization of the method is available by request to authors.