Search results for "alignment"
showing 10 items of 627 documents
GenClust: A genetic algorithm for clustering gene expression data
2005
Abstract Background Clustering is a key step in the analysis of gene expression data, and in fact, many classical clustering algorithms are used, or more innovative ones have been designed and validated for the task. Despite the widespread use of artificial intelligence techniques in bioinformatics and, more generally, data analysis, there are very few clustering algorithms based on the genetic paradigm, yet that paradigm has great potential in finding good heuristic solutions to a difficult optimization problem such as clustering. Results GenClust is a new genetic algorithm for clustering gene expression data. It has two key features: (a) a novel coding of the search space that is simple, …
Copy number variation and missense mutations of the agouti signaling protein (ASIP) gene in goat breeds with different coat colors.
2009
In goats, classical genetic studies reported a large number of alleles at the Agouti locus with effects on coat color and pattern distribution. From these early studies, the dominant A(Wt) (white/tan) allele was suggested to cause the white color of the Saanen breed. Here, we sequenced the coding region of the goat ASIP gene in 6 goat breeds (Girgentana, Maltese, Derivata di Siria, Murciano-Granadina, Camosciata delle Alpi, and Saanen), with different coat colors and patterns. Five single nucleotide polymorphisms (SNPs) were identified, 3 of which caused missense mutations in conserved positions of the cysteine-rich carboxy-terminal domain of the protein (p.Ala96Gly, p.Cys126Gly, and p.Val1…
Approximation of functions over manifolds : A Moving Least-Squares approach
2021
We present an algorithm for approximating a function defined over a $d$-dimensional manifold utilizing only noisy function values at locations sampled from the manifold with noise. To produce the approximation we do not require any knowledge regarding the manifold other than its dimension $d$. We use the Manifold Moving Least-Squares approach of (Sober and Levin 2016) to reconstruct the atlas of charts and the approximation is built on-top of those charts. The resulting approximant is shown to be a function defined over a neighborhood of a manifold, approximating the originally sampled manifold. In other words, given a new point, located near the manifold, the approximation can be evaluated…
Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment.
2007
Abstract Background Similarity of sequences is a key mathematical notion for Classification and Phylogenetic studies in Biology. It is currently primarily handled using alignments. However, the alignment methods seem inadequate for post-genomic studies since they do not scale well with data set size and they seem to be confined only to genomic and proteomic sequences. Therefore, alignment-free similarity measures are actively pursued. Among those, USM (Universal Similarity Metric) has gained prominence. It is based on the deep theory of Kolmogorov Complexity and universality is its most novel striking feature. Since it can only be approximated via data compression, USM is a methodology rath…
Efficient and Accurate OTU Clustering with GPU-Based Sequence Alignment and Dynamic Dendrogram Cutting.
2015
De novo clustering is a popular technique to perform taxonomic profiling of a microbial community by grouping 16S rRNA amplicon reads into operational taxonomic units (OTUs). In this work, we introduce a new dendrogram-based OTU clustering pipeline called CRiSPy. The key idea used in CRiSPy to improve clustering accuracy is the application of an anomaly detection technique to obtain a dynamic distance cutoff instead of using the de facto value of 97 percent sequence similarity as in most existing OTU clustering pipelines. This technique works by detecting an abrupt change in the merging heights of a dendrogram. To produce the output dendrograms, CRiSPy employs the OTU hierarchical clusterin…
Sorting signals in the cytosolic tail of membrane proteins involved in the interaction with plant ARF1 and coatomer.
2004
Summary In mammals and yeast, a cytosolic dilysine motif is critical for endoplasmic reticulum (ER) localization of type I membrane proteins. Retrograde transport of type I membrane proteins containing dilysine motifs at their cytoplasmic carboxy (C)-terminal tail involves the interaction of these motifs with the COPI coat. The C-terminal dilysine motif has also been shown to confer ER localization to type I membrane proteins in plant cells. Using in vitro binding assays, we have analyzed sorting motifs in the cytosolic tail of membrane proteins, which may be involved in the interaction with components of the COPI coat in plant cells. We show that a dilysine motif in the −3,−4 position (rel…
The generalizability of Older Adult Self-Report (OASR) syndromes of psychopathology across 20 societies
2020
Contains fulltext : 217516.pdf (Publisher’s version ) (Closed access) Objectives: As the world population ages, psychiatrists will increasingly need instruments for measuring constructs of psychopathology that are generalizable to diverse elders. The study tested whether syndromes of co-occurring problems derived from self-ratings of psychopathology by US elders would fit self-ratings by elders in 19 other societies. Methods/design: The Older Adult Self-Report (OASR) was completed by 12 826 adults who were 60 to 102 years old in 19 societies from North and South America, Asia, and Eastern, Northern, Southern, and Western Europe, plus the United States. Individual and multigroup confirmatory…
Multimodal accomplishment of alignment and affiliation in the local space of distant meetings
2017
Technology-mediated (i.e. distant) meetings are complex settings that involve distributed participation frameworks and the coordination of actions in multiple interactional spaces. This paper examines how problems with hearing, speaking, or understanding in the overall meeting space enable the negotiation of alignment and affiliation by co-present participants in the same local meeting space. Conversation analysis is used to investigate the local accomplishment of alignment and affiliation achieved through the sequential and temporal organization of verbal, embodied, and material resources of interaction in three types of situations: during technological trouble, silences, and disagreements…
Changes in membrane lipid composition in ethanol- and acid-adapted Oenococcus oeni cells: characterization of the cfa gene by heterologous complement…
2008
International audience; Cyclopropane fatty acid (CFA) synthesis was investigated in Oenococcus oeni. The data obtained demonstrated that acid-grown cells or cells harvested in the stationary growth phase showed changes in fatty acid composition similar to those of ethanol-grown cells. An increase of the CFA content and a decrease of the oleic acid content were observed. The biosynthesis of CFAs from unsaturated fatty acid phospholipids is catalysed by CFA synthases. Quantitative real-time-PCR experiments were performed on the cfa gene of O. oeni, which encodes a putative CFA synthase. The level of cfa transcripts increased when cells were harvested in stationary phase and when cells were gr…
MIF from mussel: coding sequence, phylogeny, polymorphism, 3D model and regulation of expression.
2012
Abstract Three macrophage migration inhibitory factor (MIF)-related sequences were identified from a Mytilus galloprovincialis EST library. The consensus sequence included a 5′-UTR of 32 nucleotides, the complete ORF of 345 nucleotides, and a 3′-UTR of 349 nucleotides. As for other MIFs, M. galloprovincialis ORF does not include any signal or C-terminus extensions. The translated sequence of 115 amino acids possesses a molecular mass of 12,681.4, a pI of 6.27 and a stability index of 21.48. Its 3D structure resembles human MIF except for one shorter α-helix. Although evolutionary separated from ticks and vertebrates, Mg-MIF appeared to be closely related to Pinctada fucata and Haliotis, but…