基因组学
We precisely position a noncanonical intron in the odd second copy of tRNAAsp(GTC) gene in the newly sequenced crenarchaea S.acidocaldarius. The uniform assortment of some features from normal aspartate tDNA and some from those…
Based upon the correlation matrix of the human promoter sequences, a complex network is constructed to capture the principal relationships between these promoters. It is a complex network has the properties of the right-skewed degree…
We show that simple stochastic models of genome evolution lead to power law asymptotics of protein domain family size distribution. These models, called Birth, Death and Innovation Models (BDIM), represent a special class of balanced…
In our previous studies, we developed discrete-space Birth, Death and Innovation Models (BDIM) of genome evolution. These models explain the origin of the characteristic Pareto distribution of paralogous gene family sizes in genomes, and…
A number of recent studies have hypothesized that sense-antisense RNA transcript pairs create dsRNA duplexes that undergo extensive A-to-I RNA editing. Here we studied human and mouse genomic antisense regions, and found that the editing…
Background: Recent studies in a growing number of organisms have yielded accumulating evidence that a significant portion of the non-coding region in the genome is transcribed. We address this issue in the yeast Saccharomyces cerevisiae.…
Features unique to a transfer-RNA are recognized by the corresponding tRNA-synthetase. Keeping this in view we isolate the discriminating features of all archaeal tRNA. These are our identity elements. Further, we investigate…
We analyse forty seven chloroplastid genes of the large subunit of RuBisCO, from the Algal order Ectocarpales, sourced from GenBank. Codon-usage weighted by the nucleotide base bias defines our score called the Codon-Impact-Parameter. This…
Gene duplication is key to molecular evolution in all three domains of life and may be the first step in the emergence of new gene function. It is a well recognized feature in large DNA viruses, but has not been studied extensively in the…
In this paper we present a collection of results pertaining to haplotyping. The first set of results concerns the combinatorial problem of reconstructing haplotypes from incomplete and/or imperfectly sequenced haplotype data. More…
By means of the nonlinear modeling technique (NM technique), we find the nonlinear deterministic structures in the promoter regions (PPRs) of DNA sequences, called deterministic valleys (DVs) in this paper. These DVs prefer to occur much…
We discuss a simple and powerful approach for the ab initio identification of cis-regulatory motifs involved in transcriptional regulation. The method we present integrates several elements: human-mouse comparison, statistical analysis of…
The recent algorithm for five split tRNA-genes in N.equitans is new . It locates missing tRNA-trp, tRNA-imet, tRNA-glu and tRNA-his . But the split tRNA-trp(CCA) solution is anomalous ; the tRNA-imet lacks cognition elements for…
We study the electronic properties of DNA by way of a tight-binding model applied to four particular DNA sequences. The charge transfer properties are presented in terms of localisation lengths, crudely speaking the length over which…
Information valuable words are the strings with the significant deviation of real frequency from the expected one. The expected frequency is determined through the maximum entropy principle of the reconstructed (extended) frequency…
A-to-I RNA editing by ADARs is a post-transcriptional mechanism for expanding the proteomic repertoire. Genetic recoding by editing was so far observed for only a few mammalian RNAs that are predominantly expressed in nervous tissues.…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
Network of packages with regulatory interactions (dependences and conflicts) from Debian GNU/Linux operating system is compiled and used as analogy of a gene regulatory network. Using a trace-back algorithm we assembly networks from the…
This study presents the first global, 1 Mbp level analysis of patterns of nucleotide substitutions along the human lineage. The study is based on the analysis of a large amount of repetitive elements deposited into the human genome since…
The presence of neighbor dependencies generated a specific pattern of dinucleotide frequencies in all organisms. Especially, the CpG-methylation-deamination process is the predominant substitution process in vertebrates and needs to be…