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Large-scale parallel alignment of platelet-shaped particles through gravitational sedimentation.

ABSTRACT: Parallel and concentric alignment of microscopic building blocks into several orders of magnitude larger structures is commonly observed in nature. However, if similarly aligned structures are artificially produced their thickness is generally limited to just about one or two orders of magnitude more than the dimensions of the smallest element. We show that sedimentation provides a promising approach to manufacture solid materials consisting of well-aligned platelet-shaped particles while being more than 30,000 times thicker than the individual particle. Such sediments contain up to 28 vol% of particles without any further treatment and can be densified to 67 vol% particle fraction by subsequent unidirectional pressing. The degree of orientation of the platelet-shaped particles within the sediments was tracked by high-energy X-ray diffraction measurements. The Hermans orientation parameter, a statistical measure of the quality of alignment, was determined to be 0.63 ± 0.03 already for as-sedimented samples while the standard deviation of the orientation distribution of particles, another measure of average misalignment, was found to be (21.5 ± 1.4)°. After pressing, these values further improved to (0.81 ± 0.01) and (14.6 ± 0.4)°, respectively. Such quality of alignment competes with, if not even exceeds, values reported in the literature.

SUBMITTER: Behr S

PROVIDER: S-EPMC4435022 | biostudies-other | 2015

REPOSITORIES: biostudies-other

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Project description:BACKGROUND: Metagenomics is a powerful methodology to study microbial communities, but it is highly dependent on nucleotide sequence similarity searching against sequence databases. Metagenomic analyses with next-generation sequencing technologies produce enormous numbers of reads from microbial communities, and many reads are derived from microbes whose genomes have not yet been sequenced, limiting the usefulness of existing sequence similarity search tools. Therefore, there is a clear need for a sequence similarity search tool that can rapidly detect weak similarity in large datasets. RESULTS: We developed a tool, which we named CLAST (CUDA implemented large-scale alignment search tool), that enables analyses of millions of reads and thousands of reference genome sequences, and runs on NVIDIA Fermi architecture graphics processing units. CLAST has four main advantages over existing alignment tools. First, CLAST was capable of identifying sequence similarities ~80.8 times faster than BLAST and 9.6 times faster than BLAT. Second, CLAST executes global alignment as the default (local alignment is also an option), enabling CLAST to assign reads to taxonomic and functional groups based on evolutionarily distant nucleotide sequences with high accuracy. Third, CLAST does not need a preprocessed sequence database like Burrows-Wheeler Transform-based tools, and this enables CLAST to incorporate large, frequently updated sequence databases. Fourth, CLAST requires <2 GB of main memory, making it possible to run CLAST on a standard desktop computer or server node. CONCLUSIONS: CLAST achieved very high speed (similar to the Burrows-Wheeler Transform-based Bowtie 2 for long reads) and sensitivity (equal to BLAST, BLAT, and FR-HIT) without the need for extensive database preprocessing or a specialized computing platform. Our results demonstrate that CLAST has the potential to be one of the most powerful and realistic approaches to analyze the massive amount of sequence data from next-generation sequencing technologies.

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Large-scale parallel alignment of platelet-shaped particles through gravitational sedimentation.

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