In Silico Verification of Predicted Potential Promoter Sequences in the Rice () Genome.

The exact identification of promoter sequences remains a serious problem in computational biology, as the promoter prediction algorithms under development continue to produce false-positive results. Therefore, to fully assess the validity of predicted sequences, it is necessary to perform a comprehensive test of their properties, such as the presence of downstream transcribed DNA regions behind them, or chromatin accessibility for transcription factor binding. In this paper, we examined the promoter sequences of chromosome 1 of the rice genome from the Database of Potential Promoter Sequences predicted using a mathematical algorithm based on the derivation and calculation of statistically significant promoter classes.

Application of the MAHDS Method for Multiple Alignment of Highly Diverged Amino Acid Sequences.

The aim of this work was to compare the multiple alignment methods MAHDS, T-Coffee, MUSCLE, Clustal Omega, Kalign, MAFFT, and PRANK in their ability to align highly divergent amino acid sequences. To accomplish this, we created test amino acid sequences with an average number of substitutions per amino acid (x) from 0.6 to 5.

Detection of Highly Divergent Tandem Repeats in the Rice Genome.

Currently, there is a lack of bioinformatics approaches to identify highly divergent tandem repeats (TRs) in eukaryotic genomes. Here, we developed a new mathematical method to search for TRs, which uses a novel algorithm for constructing multiple alignments based on the generation of random position weight matrices (RPWMs), and applied it to detect TRs of 2 to 50 nucleotides long in the rice genome. The RPWM method could find highly divergent TRs in the presence of insertions or deletions.

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.

Database of Periodic DNA Regions in Major Genomes.

. We analyzed several prokaryotic and eukaryotic genomes looking for the periodicity sequences availability and employing a new mathematical method. The method envisaged using the random position weight matrices and dynamic programming.

Developing of the Computer Method for Annotation of Bacterial Genes.

Over the last years a great number of bacterial genomes were sequenced. Now one of the most important challenges of computational genomics is the functional annotation of nucleic acid sequences. In this study we presented the computational method and the annotation system for predicting biological functions using phylogenetic profiles.

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.

An approach for searching insertions in bacterial genes leading to the phase shift of triplet periodicity.

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).

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.

Study of the triplet periodicity phase shifts in genes.

The definition of a phase shift of triplet periodicity (TP) is introduced. The mathematical algorithm for detection of TP phase shift of nucleotide sequences has been developed. Gene sequences from Kegg-46 data bank were analyzed with a purpose of searching genes with a phase shift of TP.

Latent periodicity of protein families, identified with the indel-aware algorithm.

Latent amino acid repeats seem to be widespread in genetic sequences and to reflect their structure, function, and evolution. We have recently identified latent periodicity in more than 150 protein families including protein kinases and various nucleotide-binding proteins. The latent repeats in these families were correlated to their structure and evolution.

Identification of amino acid latent periodicity within 94 protein families.

Here, we have applied information decomposition, cyclic profile alignment, and noise decomposition techniques to search for latent repeats within protein families of various functions. We have identified 94 protein families with a family-specific periodicity. In each case, the periodic element was found in greater than 70% of family members.

Latent periodicity of serine-threonine and tyrosine protein kinases and other protein families.

We identified latent periodicity in catalytic domains of approximately 85% of annotated serine-threonine and tyrosine protein kinases. Similar results were obtained for other 22 protein families and domains. We also designed the method of noise decomposition, which is aimed to distinguish between different periodicity types of the same period length.

Evolution of tRNA-like sequences and genome variability.

Transfer RNA (tRNA)-like sequences were searched for in the nine basic taxonomic divisions of GenBank-121 (viruses, phages, bacteria, plants, invertebrates, vertebrates, rodents, mammals, and primates) by an original program package implementing a dynamic profile alignment approach for the genetic texts' analysis, in using 22 profiles of tRNAs of different isotypes. In total, 175,901 previously unknown tRNA-like sequences were revealed. The locations of the tRNA-likes were considered over the regions whose functional meaning is described by standard Feature Keys in GenBank.