Motivation: In literature, several transformations exists to obtain a new cumulative distribution function (cdf) using other(s) well-known cdf(s). Results: In this note we find applications of some new cumulative distribution function transformations to construct a family of sigmoidal functions based on the Verhulst logistic function. We prove estimates for the Hausdorff approximation of the shifted Heaviside step function by means of this family. Numerical examples, illustrating our results are given. JOURNAL OF BIOINFORMATICS AND GENOMICS, No. 1 (3) (2017)

The scutes located on the carapace of the red-eared slider Trachemys scripta elegans (Wied-Neuwied, 1839) have been modeled. Bioinformatics modeling of carapace’s scutes were carried out by utilizing the Voronoi decomposition and Delaunay triangulation method. These two geometric techniques allow the patterns of vertebral and costal scutes to be recreated. The proposed model may have a certain value for taxonomy as well as for estimating the symmetry of the morphological structures, which is important for the purposes of biomimetics. JOURNAL OF BIOINFORMATICS AND GENOMICS, No. 3 (5) (2017)

Currently existing methods and parameters are inadequate for representative and quanititative assessment of cytotoxic activity of chemical compounds. Recently, we have introduced a concept of cytotoxic power which provides an effective way to a reasonable estimation and comparative analysis of cytotoxic activity of chemical agents. The basis of this concept is an integrative parameter that relies on important toxicological principles: dose of compound related to a cell number and exposure-time-response relationship of its activity. Herein, we propose an implementation of our concept of cytotoxic power as a package developed in Python programming language. The package is free and available on GitHub repository. JOURNAL OF BIOINFORMATICS AND GENOMICS, No. 4 (9) (2018)

A brief review is given of recent advances in the taxonomic study of organisms and current views on biological evolution and the origin of life. A discussion is presented on how the treelike and net components contribute to the topology of phylogenetic constructs, with account taken of the prevailing role of horizontal gene transfer in prokaryote evolution and life. Approaches are described to the rational selection and practical use of phylogenetic markers (including 16S rRNA gene DNA sequences) in biomedical (including metagenomic) applications with traditional and nontraditional (large) amounts of molecular genetic data. Emerging results from taxonomic studies of the Earth’s biota and the methods of their generation are demonstrated. It is noted that the current developments in particle physics and in cosmology have important implications for solving paradoxes associated with the vanishingly small probability of some fundamental processes of prebiological and biological evolution. Journal of Bioinformatics and Genomics, No 1 (1) (2016)

A brief review is given of recent advances in the taxonomic study of organisms and current views on biological evolution and the origin of life. A discussion is presented on how the treelike and net components contribute to the topology of phylogenetic constructs, with account taken of the prevailing role of horizontal gene transfer in prokaryote evolution and life. Approaches are described to the rational selection and practical use of phylogenetic markers (including 16S rRNA gene DNA sequences) in biomedical (including metagenomic) applications with traditional and nontraditional (large) amounts of molecular genetic data. Emerging results from taxonomic studies of the Earth’s biota and the methods of their generation are demonstrated. It is noted that the current developments in particle physics and in cosmology have important implications for solving paradoxes associated with the vanishingly small probability of some fundamental processes of prebiological and biological evolution. JOURNAL OF BIOINFORMATICS AND GENOMICS, No. 1 (1) (2016)

The most general model of a pairwise global alignment with the possibility of aligning long sequences is considered. The model features are alignment of sequences in different alphabets including nucleotides and amino acids, alternative alignments with the same score, predefined or fully customazible scoring matrix and gap penalty systems for each sequence including end gap penalties. Developed versatile parallel algorithm for global alignment is based on the Needleman-Wunsch algorithm with an arbitrary scoring matrix and Gotoh algorithm for the affine system of penalties for gaps. The main features of the algorithm include optimal memory consumption and parallel computation. It is proved that algorithm can align two sequences of length in memory space . The algorithm is implemented in the form of a high-performance web application in Javascript programming language with the usage of webworkers and is freely available on http://sbars.impb.ru/aligner.html. JOURNAL OF BIOINFORMATICS AND GENOMICS, No. 1 (10) (2019)

Motivation: The human microbiome plays an important role in human health and disease. The composition of the human microbiome is influenced by multiple factors and understanding these factors is critical to elucidate the role of the microbiome in health and disease and for development of new diagnostics or therapeutic targets based on the microbiome. 16S ribosomal RNA (rRNA) gene targeted amplicon sequencing is a commonly used approach to determine the taxonomic composition of the bacterial community. Operational taxonomic units (OTUs) are clustered based on generated sequence reads and used to determine whether and how the abundance of microbiome is correlated with some characteristics of the samples, such as health/disease status, smoking status, or dietary habit. However, OTU count data is not only overdispersed but also contains an excess number of zero counts due to undersampling. Efficient analytical tools are therefore needed for downstream statistical analysis which can simultaneously account for overdispersion and sparsity in microbiome data. JOURNAL OF BIOINFORMATICS AND GENOMICS, No. 2 (2) (2016)

Motivation: The browser-based visualization of Hi-C contact maps alongside complementary data tracks is a computationally challenging task and requires an efficient software implementation to run on small clients. Few software packages have yet been shared with the community to address this problem and modification of these is cumbersome. Results: We introduce Bekvaem that addresses these problems by using high-level Python interfaces. Wrapping several libraries for online visualizations at the front-end and the organization of large biological data sets at the server-side allows for setting up a high-performance user-defined browser visualization for Hi-C data with just a few changes in the code. Availability and implementation: The source code, written in Python, of Bekvaem alongside its documentation and sample data is freely available on heiDATA . A demonstration server is available here . JOURNAL OF BIOINFORMATICS AND GENOMICS, No. 2 (11) (2019)

Summary: A simple-to-use Java-based software package CelNetAnalyzer was developed. CelNetAnalyzer is managed through a graphical user interface and it returns a comprehensive list of the topological indices including compositional complexity, degree and neighbourhood, clustering, distance, centrality and heterogeneity indices as well as simple cycles and Shannon information entropy of undirected networks. Comparative studies have shown that due to parallelization and use of enhanced and newly developed algorithms, CelNetAnalyzer calculates these parameters significantly faster than competitors. Availability and Implementation: CelNetAnalyzer is an open-source project and free distributed for non-commercial use. Software package, source code, test network and the results of the topological analysis can be downloaded from website of the Department of Genetics at Belarusian State University (http://bio.bsu.by/genetics/grinev_software.html). Supplementary information: Supplementary data are available at Journal of Bioinformatics and Genomics online. JOURNAL OF BIOINFORMATICS AND GENOMICS, No. 1 (3) (2017)

The structure of noncoding RNAs largely determines their functions. With the rapid growth of experimental data on the RNA secondary structures, the task of predicting its spatial structure becomes the most urgent task of RNA bioinformatics. The ability to predict tertiary base pairs from data on the secondary structure could significantly reduce the operating time and improve the quality of the RNA spatial structure prediction algorithms. In this work, we applied the machine learning algorithm for the problem of RNA tertiary base pairs prediction from data on the RNA sequence and secondary structure. A group of local base pairs was identified that can be predicted with high quality (80% precision, 80% recall). It was also shown that more than 70% of all long-range noncanonical base pairs in RNA are the base pairs of geometric classes Sugar-Edge/Sugar-Edge and Sugar-Edge/Watson-Crick-Edge that correspond to ribose zipper and A-minor tertiary motifs. JOURNAL OF BIOINFORMATICS AND GENOMICS, No. 1 (13) (2020)