Search results for "sequence"
showing 10 items of 4987 documents
Sequence stratigraphy and paleo-oceanography of an open-marine mixed carbonate/siliciclastic succession (Late Jurassic, Southern Germany)
1992
The Late Jurassic epicontinental sea of South Germany protruded far to the North forming a wide bay which was rimmed by shallow-water platforms (Swiss and French Jura). This wide shelf is characterized by extensive downslope mud accumulations including siliceous sponge buildups. The bioherms are aligned along the more pericontinental parts of this shelf, which graded to the South into the Helvetic Basin of the Tethys Ocean.
Massive presence of insertion sequences in the genome of SOPE, the primary endosymbiont of the rice weevil Sitophilus oryzae
2008
Bacteria that establish an obligate intracellular relationship with eukaryotic hosts undergo an evolutionary genomic reductive process. Recent studies have shown an increase in the number of mobile elements in the first stage of the adaptive process towards intracellular life, although these elements are absent in ancient endosymbionts. Here, the genome of SOPE, the obligate mutualistic endosymbiont of rice weevils, was used as a model to analyze the initial events that occur after symbiotic integration. During the first phases of the SOPE genome project, four different types of insertion sequence (IS) elements, belonging to well-characterized IS families from γ-proteobacteria, were identif…
Cyclicity of common slow–fast cycles
2011
Abstract We study the limit cycles of planar slow–fast vector fields, appearing near a given slow–fast cycle, formed by an arbitrary sequence of slow parts and fast parts, and where the slow parts can meet the fast parts in a nilpotent contact point of arbitrary order. Using the notion slow divergence integral, we delimit a large subclass of these slow–fast cycles out of which at most one limit cycle can perturb, and a smaller subclass out of which exactly one limit cycle will perturb. Though the focus lies on common slow–fast cycles, i.e. cycles with only attracting or only repelling slow parts, we present results that are valid for more general slow–fast cycles. We also provide examples o…
The crystal structure of bacteriophage Qβ at 3.5 å resolution
1996
Abstract Background: The capsid protein subunits of small RNA bacteriophages form a T=3 particle upon assembly and RNA encapsidation. Dimers of the capsid protein repress translation of the replicase gene product by binding to the ribosome binding site and this interaction is believed to initiate RNA encapsidation. We have determined the crystal structure of phage Qβ with the aim of clarifying which factors are the most important for particle assembly and RNA interaction in the small phages. Results The crystal structure of bacteriophage Qβ determined at 3.5 a resolution shows that the capsid is stabilized by disulfide bonds on each side of the flexible loops that are situated around the fi…
unitas: the universal tool for annotation of small RNAs
2017
AbstractBackgroundNext generation sequencing is a key technique in small RNA biology research that has led to the discovery of functionally different classes of small non-coding RNAs in the past years. However, reliable annotation of the extensive amounts of small non-coding RNA data produced by high-throughput sequencing is time-consuming and requires robust bioinformatics expertise. Moreover, existing tools have a number of shortcomings including a lack of sensitivity under certain conditions, limited number of supported species or detectable sub-classes of small RNAs.ResultsHere we introduce unitas, an out-of-the-box ready software for complete annotation of small RNA sequence datasets, …
SWAPHI: Smith-Waterman Protein Database Search on Xeon Phi Coprocessors
2014
The maximal sensitivity of the Smith-Waterman (SW) algorithm has enabled its wide use in biological sequence database search. Unfortunately, the high sensitivity comes at the expense of quadratic time complexity, which makes the algorithm computationally demanding for big databases. In this paper, we present SWAPHI, the first parallelized algorithm employing Xeon Phi coprocessors to accelerate SW protein database search. SWAPHI is designed based on the scale-and-vectorize approach, i.e. it boosts alignment speed by effectively utilizing both the coarse-grained parallelism from the many co-processing cores (scale) and the fine-grained parallelism from the 512-bit wide single instruction, mul…
Algorithms for Graph and Network Analysis: Graph Alignment
2019
In this article we discuss the problem of graph alignment, which has been longly referred to for the purpose of analyzing and comparing biological networks. In particular, we describe different facets of graph alignment, according to the number of input networks, the fixed output objective, the possible heterogeneity of input data. Accordingly, we will discuss pairwise and multiple alignment, global and local alignment, etc. Moreover, we provide a comprehensive overview of the algorithms and techniques proposed in the literature to solve each of the specific considered types of graph alignment. In order to make the material presented here complete and useful to guide the reader in the use o…
GSWABE: faster GPU-accelerated sequence alignment with optimal alignment retrieval for short DNA sequences
2014
In this paper, we present GSWABE, a graphics processing unit GPU-accelerated pairwise sequence alignment algorithm for a collection of short DNA sequences. This algorithm supports all-to-all pairwise global, semi-global and local alignment, and retrieves optimal alignments on Compute Unified Device Architecture CUDA-enabled GPUs. All of the three alignment types are based on dynamic programming and share almost the same computational pattern. Thus, we have investigated a general tile-based approach to facilitating fast alignment by deeply exploring the powerful compute capability of CUDA-enabled GPUs. The performance of GSWABE has been evaluated on a Kepler-based Tesla K40 GPU using a varie…
Holomorphic approximation of ultradifferentiable functions
1981
Introduct ion Let S be a closed subset of some open set in Cn and denote by dT(S) the space of germs of holomorphic functions on (a neighborhood of) S. For a space F(S) of tEvalued (continuous, differentiable etc.) functions on S [containing t~(S)] the problem of holomorphic approximation consists of finding conditions to ensure that the natural mapping Q : e)(S)-~F(S) has dense range with respect to a given topology on F(S). Positive solutions for F = C r, 0_ l . For Q:tP(/3)~O(D)c~C(/3), DCIE n strongly pseudoconvex, proofs were given independently by Henkin [17], Kerzman [21], and Lieb [27], for the case e : (9(/3)~(9(D)c~C~(/3) cf. also [30] and for Sobolev spaces see Bell [3, Sect. 6].…
Accurate Judgments of Neuroticism at Zero Acquaintance: A Question of Relevance
2014
Prior studies have consistently found a surprising inaccuracy of people's neuroticism judgments at zero acquaintance. Based on the Realistic Accuracy Model (Funder, 1995), we hypothesize that this is due to a lack of relevance of the situation in which targets are typically observed. Fifty participants were videotaped in a highly trait-relevant (i.e., socially stressful) situation as well as three less relevant situations. An aggregate of self-reports and informant reports was used as the accuracy criterion. Four independent groups of unacquainted observers judged participants' neuroticism based on these short video sequences. Results showed that neuroticism judgments were significantly mor…