Related papers: Non-alignment comparison of human and high primate…
Genomic evolution can be viewed as string-editing processes driven by mutations. An understanding of the statistical properties resulting from these mutation processes is of value in a variety of tasks related to biological sequence data,…
In genome-wide interaction studies, to detect gene-gene interactions, most methods are divided into two folds: single nucleotide polymorphisms (SNP) based and gene-based methods. Basically, the methods based on the gene are more effective…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
High signal to noise ratio (SNR) consistency of model selection criteria in linear regression models has attracted a lot of attention recently. However, most of the existing literature on high SNR consistency deals with model order…
Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realized by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free…
We propose a novel combination of methods that (i) portrays quantitative characteristics of a DNA sequence as an image, (ii) computes distances between these images, and (iii) uses these distances to output a map wherein each sequence is a…
Frameshift translation is an important phenomenon that contributes to the appearance of novel Coding DNA Sequences (CDS) and functions in gene evolution, by allowing alternative amino acid translations of genes coding regions. Frameshift…
Measuring natural selection on genomic elements involved in the cis-regulation of gene expression -- such as transcriptional enhancers and promoters -- is critical for understanding the evolution of genomes, yet it remains a major…
Estimating the phylogeny of the genus Homo is entering a new phase of vastly improved data and methodology. There is increasing evidence of 6 to 10 competing species/lineages at any point in the last half million years, making the…
We propose a new alignment-free algorithm by constructing a compact vector representation on $\mathbb{R}^{24}$ of a DNA sequence of arbitrary length. Each component of this vector is obtained from a representative sequence, the elements of…
We provide, on an extensive dataset and using several different distances, confirmation of the hypothesis that CGR patterns are preserved along a genomic DNA sequence, and are different for DNA sequences originating from genomes of…
Associating genetic markers with a multidimensional phenotype is an important yet challenging problem. In this work, we establish the equivalence between two popular methods: kernel-machine regression (KMR), and kernel distance covariance…
GC-content, the ratio of guanine and cytosine bases in an entire nucleotide sequence, and palindromic sequences are unique for every organism due to genomic evolution. The goals of our research was to establish a correlation between…
The macromolecules that encode and translate information in living systems, DNA and RNA, exhibit distinctive structural asymmetries, including homochirality or mirror image asymmetry and $3' - 5'$ directionality, that are invariant across…
Metagenome, a mixture of different genomes (as a rule, bacterial), represents a pattern, and the analysis of its composition is, currently, one of the challenging problems of bioinformatics. In the present study, the possibility of…
Genomic subsequences conserved between closely related species such as human and chimpanzee exhibit an exponential length distribution, in contrast to the algebraic length distribution observed for sequences shared between distantly related…
Background. The large-scale pattern of distribution of genes on the chromosomes in the known animal genomes is not well characterized. We hypothesized that individual genes will be distributed on chromosomes in a mathematically ordered…
Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…
Tools that effectively analyze and compare sequences are of great importance in various areas of applied computational research, especially in the framework of molecular biology. In the present paper, we introduce simple geometric criteria…
Deep regression models typically learn in an end-to-end fashion without explicitly emphasizing a regression-aware representation. Consequently, the learned representations exhibit fragmentation and fail to capture the continuous nature of…