Minimal Absent Words in Rooted and Unrooted Trees

We extend the theory of minimal absent words to (rooted and unrooted) trees, having edges labeled by letters from an alphabet of cardinality. We show that the set of minimal absent words of a rooted (resp. unrooted) tree T with n nodes has cardinality (resp.), and we show that these bounds are realized. Then, we exhibit algorithms to compute all minimal absent words in a rooted (resp. unrooted) tree in output-sensitive time (resp. assuming an integer alphabet of size polynomial in n

The Information Coded in the Yeast Response Elements Accounts for Most of the Topological Properties of Its Transcriptional Regulation Network

The regulation of gene expression in a cell relies to a major extent on transcription factors, proteins which recognize and bind the DNA at specific binding sites (response elements) within promoter regions associated with each gene. We present an information theoretic approach to modeling transcriptional regulatory networks, in terms of a simple “sequence-matching” rule and the statistics of the occurrence of binding sequences of given specificity in random promoter regions. The crucial biological input is the distribution of the amount of information coded in these cognate response elements and the length distribution of the promoter regions. We provide an analysis of the transcriptional regulatory network of yeast Saccharomyces cerevisiae, which we extract from the available databases, with respect to the degree distributions, clustering coefficient, degree correlations, rich-club coefficient and the k-core structure. We find that these topological features are in remarkable agreement with those predicted by our model, on the basis of the amount of information coded in the interaction between the transcription factors and response elements

Conserved noncoding elements follow power-law-like distributions in several genomes as a result of genome dynamics

Conserved, ultraconserved and other classes of constrained elements (collectively referred as CNEs here), identified by comparative genomics in a wide variety of genomes, are non-randomly distributed across chromosomes. These elements are defined using various degrees of conservation between organisms and several thresholds of minimal length. We here investigate the chromosomal distribution of CNEs by studying the statistical properties of distances between consecutive CNEs. We find widespread power-law-like distributions, i.e. linearity in double logarithmic scale, in the inter-CNE distances, a feature which is connected with fractality and self-similarity. Given that CNEs are often found to be spatially associated with genes, especially with those that regulate developmental processes, we verify by appropriate gene masking that a power-law-like pattern emerges irrespectively of whether elements found close or inside genes are excluded or not. An evolutionary model is put forward for the understanding of these findings that includes segmental or whole genome duplication events and eliminations (loss) of most of the duplicated CNEs. Simulations reproduce the main features of the observed size distributions. Power-law-like patterns in the genomic distributions of CNEs are in accordance with current knowledge about their evolutionary history in several genomes. © 2014 Polychronopoulos et al

Analysis and classification of constrained DNA elements with N-gram graphs and genomic signatures

Most common methods for inquiring genomic sequence composition, are based on the bag-of-words approach and thus largely ignore the original sequence structure or the relative positioning of its constituent oligonucleotides. We here present a novel methodology that takes into account both word representation and relative positioning at various lengths scales in the form of n-gram graphs (NGG). We implemented the NGG approach on short vertebrate and invertebrate constrained genomic sequences of various origins and predicted functionalities and were able to efficiently distinguish DNA sequences belonging to the same species (intra-species classification). As an alternative method, we also applied the Genomic Signatures (GS) approach to the same sequences. To our knowledge, this is the first time that GS are applied on short sequences, rather than whole genomes. Together, the presented results suggest that NGG is an efficient method for classifying sequences, originating from a given genome, according to their function. © 2014 Springer International Publishing

Classification of selectively constrained DNA elements using feature vectors and rule-based classifiers

Scarce work has been done in the analysis of the composition of conserved non-coding elements (CNEs) that are identified by comparisons of two or more genomes and are found to exist in all metazoan genomes.Here we present the analysis of CNEs with a methodology that takes into account word occurrence at various lengths scales in the form of feature vector representation and rule based classifiers. We implement our approach on both protein-coding exons and CNEs, originating from human, insect ( Drosophila melanogaster) and worm (Caenorhabditis elegans) genomes, that are either identified in the present study or obtained from the literature.Alignment free feature vector representation of sequences combined with rule-based classification methods leads to successful classification of the different CNEs classes. Biologically meaningful results are derived by comparison with the genomic signatures approach, and classification rates for a variety of functional elements of the genomes along with surrogates are presented. © 2014 Elsevier Inc

Long-range correlations of RNA polymerase II promoter sequences across organisms

The statistical properties of the size distribution of DNA segments separating identical oligonucleotides are studied. For representative eukaryotes (Homo sapiens, Mus musculus, Saccharomyces cereviciae, Oryza sativa, Arabidopsis thaliana) we have demonstrated the existence of long-range correlations for the distances separating oligonucleotides of sizes 4, 5 and 6, which carry a promoter signature. This observation is independent of the consensus sequence used by the organism, as in the case of O. sativa (which mainly uses the CG promoter box) and A. thaliana (which mainly uses the TATA promoter box). If we use two parameters to characterise the size distribution separating oligonucleotides, we observe that oligonucleotides containing promoter signatures cluster together, away from the others. © 2005 Elsevier B.V. All rights reserved