Inferring the intensity of positive selection in protein-coding genes is important since it is used to shed light on the process of adaptation. Recently, it has been reported that overlapping genes, which are ubiquitous in all domains of life, seem to exhibit inordinate degrees of positive selection. Here, we present a new method for the simultaneous estimation of selection intensities in overl...

Overlapping genes (OGs) represent one type of widespread genomic feature in bacterial genomes and have been used as rare genomic markers in phylogeny inference of closely related bacterial species. However, the inference may experience a decrease in performance for phylogenomic analysis of too closely or too distantly related genomes. Another drawback of OGs as phylogenetic markers is that they...

OBJECTIVES The aims of this study were to identify small staphylococcal plasmids that carry either the trimethoprim resistance gene dfrK or the apramycin resistance gene apmA and analyse them for their structure and organization with regard to their potential role as precursors of large multiresistance plasmids that carry these genes. METHODS Trimethoprim- or apramycin-resistant staphylococci...

Overlapping structures in XML are not the symptoms of a misunderstanding of the intrinsic characteristics of a text document, nor the evidence of extreme scholarly requirements far beyond those needed by the most common XML-based applications. On the contrary, overlaps have started to appear in a large number of incredibly popular applications hidden under the guise of syntactical tricks to the...

Previous studies have suggested that the minimal cellular genome could be as small as 400 kilobases. Here, we report the complete genome sequence of the psyllid symbiont Carsonella ruddii, which consists of a circular chromosome of 159,662 base pairs, averaging 16.5% GC content. It is by far the smallest and most AT-rich bacterial genome yet characterized. The genome has a high coding density (...

A routine approach to inferring functions for a gene set is by using function enrichment analysis based on GO, KEGG or other curated terms and pathways. However, such analysis requires the existence of overlapping genes between the query gene set and those annotated by GO/KEGG. Furthermore, GO/KEGG databases only maintain a very restricted vocabulary. Here, we have developed a tool called "CoCi...

Overlapping markup refers to the issue of how to represent data structures more expressive than trees—for example direct acyclic graphs—using markup (meta-)languages which have been designed with trees in mind—for example XML. In this paper we observe that the state of the art in overlapping markup is far from being the widespread and consistent stack of standards and technologies readily avail...

Recent studies have demonstrated that gene set analysis, which tests disease association with genetic variants in a group of functionally related genes, is a promising approach for analyzing and interpreting genome-wide association studies (GWAS) data. These approaches aim to increase power by combining association signals from multiple genes in the same gene set. In addition, gene set analysis...

Most natural <span>world data involves overlapping communities where an object may belong to one or more clusters, referred as clustering. However, it is worth mentioning that these algorithms have a significant drawback. Since some of the algorithm uses k-means, also inherits characteristics being noise sensitive due arithmetic mean value which noisy can considerably influence and affect...