The objective of this paper is to show that point cloud data can under certain circumstances be clustered by strata in a plausible way. For our purposes, we consider a stratified space to be a collection of manifolds of different dimensions which are glued together in a locally trivial manner inside some Euclidean space. To adapt this abstract definition to the world of noise, we first define a...

Sequence-based prediction of protein secondary structure (SS) enjoys wide-spread and increasing use for the analysis and prediction of numerous structural and functional characteristics of proteins. The lack of a recent comprehensive and large-scale comparison of the numerous prediction methods results in an often arbitrary selection of a SS predictor. To address this void, we compare and analy...

MOTIVATION The abundance of nucleotide sequence information available has expanded horizons of inquiry for molecular evolution; however, the full potential of whole-genome analysis has not been realized because of inadequate tools. Here, we present one of the first toolkits to aid multidisciplinary high-throughput analysis. SUMMARY SPEED was created to integrate molecular evolutionary data wi...

Sequence to structure alignment is an important step in homology modeling of protein structures. Incorporation of features such as secondary structure, solvent accessibility, or evolutionary information improve sequence to structure alignment accuracy, but conventional generative estimation techniques for alignment models impose independence assumptions that make these features difficult to inc...

MOTIVATION Determining gene function is an important challenge arising from the availability of whole genome sequences. Until recently, approaches based on sequence homology were the only high-throughput method for predicting gene function. Use of high-throughput generated experimental data sets for determining gene function has been limited for several reasons. RESULTS Here a new approach is...

Previous studies of the structure and regulation of the deo operon in Escherichia coli have localized an internal regulated promoter, called deoP3, in front of the two distal genes in the operon. We report here the nucleotide sequence of the distal portion of the deoA, the deoA-deoB intercistronic region and the first part of the deoB gene, and show that deoP3 overlaps the distal segment of the...

A major hurdle to the study of microbial communities is that only about 1% of microorganisms are cultivated (Whitman et al. 1998). As such, cultureindependent approaches are necessary in order to examine the vast majority of environmental microorganisms. Many molecular techniques are available for community analysis, and most of these techniques utilize phylogenetic markers such as the 16S rRNA...

Although genes have specific phenotypic consequences in a given species, this functional relationship can clearly change during the course of evolution. Many cases of evolutionary dissociations between homologous genes and homologous morphological features are now known. These dissociations have interesting and important implications for understanding the genetic basis for evolutionary change i...

Symmetric homology of a unital algebra A over a commutative ground ring k has been defined using derived functors and the symmetric bar construction of Fiedorowicz, in an analogous way as cyclic, dihedral or quaternionic homology has been defined. In this paper, it is found that the HS∗(A) admits Dyer-Lashoff homology operations, and indeed, there is a Pontryagin product structure making HS∗(A)...