BackgroundPeriodic spacing of short adenine or thymine runs phased with DNA helical period of ~10.5 bp is associated with intrinsic DNA curvature and deformability, which play important roles in DNA-protein interactions and in the organization of chromosomes in both eukaryotes and prokaryotes. Local differences in DNA sequence periodicity have been linked to differences in gene expression in some organisms. Despite the significance of these periodic patterns, there are virtually no publicly accessible tools for their analysis.ResultsWe present novel tools suitable for assessments of DNA curvature-related sequence periodicity in nucleotide sequences at the genome scale. Utility of the present software is demonstrated on a comparison of sequence periodicities in the genomes of Haemophilus influenzae, Methanocaldococcus jannaschii, Saccharomyces cerevisiae, and Arabidopsis thaliana. The software can be accessed through a web interface and the programs are also available for download.ConclusionsThe present software is suitable for comparing DNA curvature-related sequence periodicity among different genomes as well as for analysis of intrachromosomal heterogeneity of the sequence periodicity. It provides a quick and convenient way to detect anomalous regions of chromosomes that could have unusual structural and functional properties and/or distinct evolutionary history.
Abstract-Modern ontology languages such as the Web Ontology Language (OWL) allow defining complex concepts that involve restrictions, Boolean combinations, and exhaustive enumeration of individuals. Many of the current ontology alignment algorithms either do not consider the complex concepts in their alignment procedures or model them naively, thereby producing a possibly incomplete alignment. We introduce axiomatic and graphical canonical forms for modeling value and cardinality restrictions and Boolean combinations, and present a way of measuring the similarity between these complex concepts in their canonical forms. We integrate our approach in multiple ontology alignment algorithms. Our results indicate a significant improvement in the F-measure of the alignment. However, this improvement is at the expense of increased run time due to the additional concepts modeled.
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