Maria Chaley

Profile-Statistical Periodicity of DNA Coding Regions

Novel methods for identifying a new type of DNA latent periodicity, called latent profile periodicity or latent profility, are used to search for periodic structures in genes. These methods reveal two distinct levels of organization of genetic information encoding. It is shown that latent profility in genes may correlate with specific structural features of their encoded proteins.

Statistical methods for detecting latent periodicity patterns in biological sequences: The case of small-size samples

An original spectral-statistical approach for detecting latent periodicity in biological sequences is proposed. This approach can be applied under conditions of limited statistical sample. It allows one to avoid redundancy and instability when identifying the latent periodicity structure. The optimality of the periodicity-pattern-size estimates obtained for approximate tandem repeats on the basis of the spectral-statistical approach is demonstrated in practical examples.

The Locally Optimal Method of Cyclic Alignment to Reveal Latent Periodicities in Genetic Texts: the NAD-binding Protein Sites

A program package has been developed to search for hidden tandem repeats of any specified type in the protein sequence databases. The applied algorithm of the locally optimal cyclic alignment is able to find subsequences possessing a certain profile-based periodicity type when no appreciable homology between periods is observed, as well as in the presence of arbitrary insertions/deletions. The profile can be adjusted to search for the periodicity types structurally and functionally important. The Swiss-Prot database has been analyzed to reveal the periodicities undetectable earlier that are caused by the secondary and super-secondary structure regularities of the NAD-binding sites. In particular, a significant periodicity of 24 aa was found to be characteristic of the absolute majority of domains possessing the Rossman (or Rossman-like) fold and displaying apparent regularity in their secondary structures, not being obvious at the primary structure level.

HeteroGenome: database of genome periodicity

We present the first release of the HeteroGenome database collecting latent periodicity regions in genomes. Tandem repeats and highly divergent tandem repeats along with the regions of a new type of periodicity, known as profile periodicity, have been collected for the genomes of Saccharomyces cerevisiae, Arabidopsis thaliana, Caenorhabditis elegans and Drosophila melanogaster. We obtained data with the aid of a spectral-statistical approach to search for reliable latent periodicity regions (with periods up to 2000 bp) in DNA sequences. The original two-level mode of data presentation (a broad view of the region of latent periodicity and a second level indicating conservative fragments of its structure) was further developed to enable us to obtain the estimate, without redundancy, that latent periodicity regions make up ∼10% of the analyzed genomes. Analysis of the quantitative and qualitative content of located periodicity regions on all chromosomes of the analyzed organisms revealed dominant characteristic types of periodicity in the genomes. The pattern of density distribution of latent periodicity regions on chromosome unambiguously characterizes each chromosome in genome. Database URL: http://www.jcbi.ru/lp_baze/

Stochastic model of homogeneous coding and latent periodicity in DNA sequences

The concept of latent triplet periodicity in coding DNA sequences which has been earlier extensively discussed is confirmed in the result of analysis of a number of eukaryotic genomes, where latent periodicity of a new type, called profile periodicity, is recognized in the CDSs. Original model of Stochastic Homogeneous Organization of Coding (SHOC-model) in textual string is proposed. This model explains the existence of latent profile periodicity and regularity in DNA sequences.

Revealing and Functional Analysis of Trna-Like Sequences in Various Genomes

tRNAs and their derivatives are known to be involved in various genetic processes from bacteria to primates. Revealing evolutionary ancestors and relatives of the modern tRNAs with further functional analysis could shed light on their role in expansion of interspersed repeats, their promoter activity, and so on. Although tRNA-like sequences were earlier found and described in many gene regions and most known SINE repeats contain tRNA part, there are still a lot of unknown entries. tRNA-like sequences could also help to find out new families of genetic repeats. Presence of tRNA-like sequences was detected in various genetic structures. Their relative distribution pattern over these sequences and preliminary functional analysis are presented.

Spectral–Statistical Approach for Revealing Latent Regular Structures in DNA Sequence

Methods of the spectral-statistical approach (2S-approach) for revealing latent periodicity in DNA sequences are described. The results of data analysis in the HeteroGenome database which collects the sequences similar to approximate tandem repeats in the genomes of model organisms are adduced. In consequence of further developing of the spectral-statistical approach, the techniques for recognizing latent profile periodicity are considered. These techniques are basing on extension of the notion of approximate tandem repeat. Examples of correlation of latent profile periodicity revealed in the CDSs with structural-functional properties in the proteins are given.

Statistical Methods for Detecting Latent Periodicity in Biological Sequences: Solving a Problem of Small-Size Samples

An original spectral-statistical approach for detectinglatent periodicity in biological sequences isproposed. This approach can be applied under conditionsof limited statistical sample. It allows oneto avoid redundancy and instability when identifyingthe latent periodicity structure. The resultsof spectral-statistical approach application for latentperiodicity search in genomes of model organismsare collected in the HETEROGENE databasehttp://www.jcbi.ru/ lp baze/ .