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  • 2007  (12)
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  • 2007  (12)
  • 1
    Language: English
    In: BMC Bioinformatics, May 9, 2007, Vol.8(151), p.151
    Description: Background Whole genome shotgun sequencing produces increasingly higher coverage of a genome with random sequence reads. Progressive whole genome assembly and eventual finishing sequencing is a process that typically takes several years for large eukaryotic genomes. In the interim, all sequence reads of public sequencing projects are made available in repositories such as the NCBI Trace Archive. For a particular locus, sequencing coverage may be high enough early on to produce a reliable local genome assembly. We have developed software, Tracembler, that facilitates in silico chromosome walking by recursively assembling reads of a selected species from the NCBI Trace Archive starting with reads that significantly match sequence seeds supplied by the user. Results Tracembler takes one or multiple DNA or protein sequence(s) as input to the NCBI Trace Archive BLAST engine to identify matching sequence reads from a species of interest. The BLAST searches are carried out recursively such that BLAST matching sequences identified in previous rounds of searches are used as new queries in subsequent rounds of BLAST searches. The recursive BLAST search stops when either no more new matching sequences are found, a given maximal number of queries is exhausted, or a specified maximum number of rounds of recursion is reached. All the BLAST matching sequences are then assembled into contigs based on significant sequence overlaps using the CAP3 program. We demonstrate the validity of the concept and software implementation with an example of successfully recovering a full-length Chrm2 gene as well as its upstream and downstream genomic regions from Rattus norvegicus reads. In a second example, a query with two adjacent Medicago truncatula genes as seeds resulted in a contig that likely identifies the microsyntenic homologous soybean locus. Conclusion Tracembler streamlines the process of recursive database searches, sequence assembly, and gene identification in resulting contigs in attempts to identify homologous loci of genes of interest in species with emerging whole genome shotgun reads. A web server hosting Tracembler is provided at http://www.plantgdb.org/tool/tracembler/, and the software is also freely available from the authors for local installations.
    Keywords: Genomics -- Research ; Nucleotide Sequencing -- Research
    ISSN: 1471-2105
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  • 2
    Language: English
    In: BMC Bioinformatics, 01 May 2007, Vol.8(1), p.151
    Description: Abstract Background Whole genome shotgun sequencing produces increasingly higher coverage of a genome with random sequence reads. Progressive whole genome assembly and eventual finishing sequencing is a process that typically takes several years for large eukaryotic genomes. In the interim, all sequence reads of public sequencing projects are made available in repositories such as the NCBI Trace Archive. For a particular locus, sequencing coverage may be high enough early on to produce a reliable local genome assembly. We have developed software, Tracembler, that facilitates in silico chromosome walking by recursively assembling reads of a selected species from the NCBI Trace Archive starting with reads that significantly match sequence seeds supplied by the user. Results Tracembler takes one or multiple DNA or protein sequence(s) as input to the NCBI Trace Archive BLAST engine to identify matching sequence reads from a species of interest. The BLAST searches are carried out recursively such that BLAST matching sequences identified in previous rounds of searches are used as new queries in subsequent rounds of BLAST searches. The recursive BLAST search stops when either no more new matching sequences are found, a given maximal number of queries is exhausted, or a specified maximum number of rounds of recursion is reached. All the BLAST matching sequences are then assembled into contigs based on significant sequence overlaps using the CAP3 program. We demonstrate the validity of the concept and software implementation with an example of successfully recovering a full-length Chrm2 gene as well as its upstream and downstream genomic regions from Rattus norvegicus reads. In a second example, a query with two adjacent Medicago truncatula genes as seeds resulted in a contig that likely identifies the microsyntenic homologous soybean locus. Conclusion Tracembler streamlines the process of recursive database searches, sequence assembly, and gene identification in resulting contigs in attempts to identify homologous loci of genes of interest in species with emerging whole genome shotgun reads. A web server hosting Tracembler is provided at http://www.plantgdb.org/tool/tracembler/, and the software is also freely available from the authors for local installations.
    Keywords: Biology
    ISSN: 1471-2105
    E-ISSN: 1471-2105
    Source: Directory of Open Access Journals (DOAJ)
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  • 3
    Language: English
    In: BMC bioinformatics, 09 May 2007, Vol.8, pp.151
    Description: Whole genome shotgun sequencing produces increasingly higher coverage of a genome with random sequence reads. Progressive whole genome assembly and eventual finishing sequencing is a process that typically takes several years for large eukaryotic genomes. In the interim, all sequence reads of public sequencing projects are made available in repositories such as the NCBI Trace Archive. For a particular locus, sequencing coverage may be high enough early on to produce a reliable local genome assembly. We have developed software, Tracembler, that facilitates in silico chromosome walking by recursively assembling reads of a selected species from the NCBI Trace Archive starting with reads that significantly match sequence seeds supplied by the user. Tracembler takes one or multiple DNA or protein sequence(s) as input to the NCBI Trace Archive BLAST engine to identify matching sequence reads from a species of interest. The BLAST searches are carried out recursively such that BLAST matching sequences identified in previous rounds of searches are used as new queries in subsequent rounds of BLAST searches. The recursive BLAST search stops when either no more new matching sequences are found, a given maximal number of queries is exhausted, or a specified maximum number of rounds of recursion is reached. All the BLAST matching sequences are then assembled into contigs based on significant sequence overlaps using the CAP3 program. We demonstrate the validity of the concept and software implementation with an example of successfully recovering a full-length Chrm2 gene as well as its upstream and downstream genomic regions from Rattus norvegicus reads. In a second example, a query with two adjacent Medicago truncatula genes as seeds resulted in a contig that likely identifies the microsyntenic homologous soybean locus. Tracembler streamlines the process of recursive database searches, sequence assembly, and gene identification in resulting contigs in attempts to identify homologous loci of genes of interest in species with emerging whole genome shotgun reads. A web server hosting Tracembler is provided at http://www.plantgdb.org/tool/tracembler/, and the software is also freely available from the authors for local installations.
    Keywords: Software ; Chromosome Walking -- Instrumentation ; Information Storage and Retrieval -- Methods
    E-ISSN: 1471-2105
    Source: MEDLINE/PubMed (U.S. National Library of Medicine)
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  • 4
    Description: x, 131 p.
    Description: Thesis (Ph.D.)--University of Wisconsin--Madison, 2007
    Description: Includes bibliographical references (p. 126-131)
    Description: Also available on the Internet
    Source: HathiTrust
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  • 5
    Language: English
    In: BMC Bioinformatics, London: BioMed Central Ltd.
    Description: Article discussing Tracembler, a software for in-silico chromosome walking in unassembled genomes.
    Keywords: Tracembler ; Software ; Chromosomes ; Genomes
    Source: University of North Texas
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  • 6
    Language: English
    In: ACM SIGMETRICS Performance Evaluation Review, 06/12/2007, Vol.35(1), p.253
    Description: Packet classification is the foundation of many Internet functions such as QoS and security. A long thread of research has proposed efficient software-based solutions to this problem. Such software solutions are attractive because they require cheap memory systems for implementation, thus bringing down the overall cost of the system. In contrast, hardware-based solutions use more expensive memory systems, e.g., TCAMs, but are often preferred by router vendors for their faster classification speeds. The goal of this paper is to find a "best-of-both-worlds" solution -- a solution that incurs the cost of a software-based system and has the speed of a hardware-based one. Our proposed solution, called smart rule cache achieves this goal by using minimal hardware -- a few additional registers -- to cache evolving rules which preserve classification semantics, and additional logic to match incoming packets to these rules. Using real traffic traces and real rule sets from a tier-1 ISP, we show such a setup is sufficient to achieve very high hit ratios for fast classification in hardware. Cache miss ratios are 2 ∼ 4 orders of magnitude lower than flow cache schemes. Given its low cost and good performance, we believe our solution may create significant impact on current industry practice.
    Keywords: Computer Science;
    ISBN: 9781595936394
    ISSN: 01635999
    E-ISSN: 15579484
    Source: Assciation for Computing Machinery (via CrossRef)
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  • 7
    Language: English
    In: Proceedings of the 2007 ACM SIGMETRICS international conference on measurement and modeling of computer systems, 12 June 2007, pp.253-264
    Description: Packet classification is the foundation of many Internet functions such as QoS and security. A long thread of research has proposed efficient software-based solutions to this problem. Such software solutions are attractive because they require cheap memory systems for implementation, thus bringing down the overall cost of the system. In contrast, hardware-based solutions use more expensive memory systems, e.g., TCAMs, but are often preferred by router vendors for their faster classification speeds. The goal of this paper is to find a "best-of-both-worlds" solution -- a solution that incurs the cost of a software-based system and has the speed of a hardware-based one. Our proposed solution, called 〈i〉smart rule cache〈/i〉 achieves this goal by using minimal hardware -- a few additional registers -- to cache 〈i〉evolving〈/i〉 rules which preserve classification semantics, and additional logic to match incoming packets to these rules. Using real traffic traces and real rule sets from a tier-1 ISP, we show such a setup is sufficient to achieve very high hit ratios for fast classification in hardware. Cache miss ratios are 2 ∼ 4 orders of magnitude lower than flow cache schemes. Given its low cost and good performance, we believe our solution may create significant impact on current industry practice.
    Keywords: Packet Classification ; Rule Cache ; Rule Evolution ; Computer Science
    ISBN: 9781595936394
    ISBN: 1595936394
    Source: ACM Digital Library (Association for Computing Machinery)
    Source: KESLI (ACM Digital Library)
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  • 8
    Language: English
    In: Proceedings of the 13th annual ACM international conference on mobile computing and networking, 09 September 2007, pp.306-309
    Description: Network coding is seen as a promising technique to improve network throughput. In this paper, we study two important problems in localized network coding in wireless networks, which only requires each node to know about and coordinate with one-hop neighbors. In particular, we first establish a condition that is both necessary and sufficient for useful coding to be possible. We show this condition is much weaker than expected, and hence allows a variety of coding schemes to suit different network conditions and application preferences. Based on the understanding we establish, we are able to design a robust coding technique called 〈i〉loop coding〈/i〉 that can improve network throughput and TCP throughput simultaneously.
    Keywords: Tcp ; Network Coding ; Throughput ; Wireless Networks ; Computer Science
    ISBN: 9781595936813
    ISBN: 1595936815
    Source: ACM Digital Library (Association for Computing Machinery)
    Source: KESLI (ACM Digital Library)
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  • 9
    Language: English
    In: IEEE INFOCOM 2007 - 26th IEEE International Conference on Computer Communications, May 2007, pp.2281-2285
    Description: A radio frequency identifier (RFID) system consists of inexpensive, uniquely-identifiable tags that are mounted on physical objects, and readers that track these tags (and hence these physical objects) through RF communication. In this paper we, therefore, address this load balancing problem for readers - given a set of tags that are within range of each reader, which of these tags should each reader be responsible for such that the cost for monitoring tags across the different readers is balanced, while guaranteeing that each tag is monitored by at least one reader. We show that a generalized variant of the load balancing problem is NP-hard and hence present a 2-approximation centralized algorithm. We next present an optimal centralized solution for a specialized variant. Subsequently, we present a localized distributed algorithm that is probabilistic in nature and closely matches the performance of the centralized algorithms. Our results demonstrate that our schemes achieve very good performance even in highly dynamic large-scale RFID systems.
    Keywords: Load Management ; Large-Scale Systems ; Radiofrequency Identification ; Monitoring ; Costs ; Radio Frequency ; USA Councils ; Peer to Peer Computing ; Rfid Tags ; Information Retrieval ; Engineering
    ISBN: 1424410479
    ISBN: 9781424410477
    ISSN: 0743166X
    Source: IEEE Conference Publications
    Source: IEEE Xplore
    Source: IEEE Journals & Magazines 
    Source: IEEE eBooks
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  • 10
    In: 润滑与密封 - Lubrication Engineering, 2007, Vol.32(10), pp.25-28
    Description: 以高纯石墨作靶材、N2/Ar为工作气体,采用非平衡磁控溅射技术在高速钢上制备了光滑、致密、均匀的掺氮DLC膜。用XPS、Raman光谱仪表征了DLC膜的结构,并在球一盘摩擦试验机上研究了其摩擦特性。结果表明:工作气体中的N2比例对DLC膜结构及其摩擦特性影响较大,随着N2比例的增加薄膜中sp^3的比例减少,而sp^3和碳氮键的比例增加;随着N2比例的增加,薄膜摩擦因数先减后增,这与薄膜中sp^3比例下降和sp^3比例增加而导致薄膜的硬度以及内应力变化有关。就本试验而言,工作气体中N2比例不应高于20%。
    Description: Diamond-like carbon (DLC) films doped with nitrogen atoms were deposited on high speed steel at room temperature prepared by unbalanced magnetron sputtering method with NJAr as working gases and high purity graphite as a target. Surface of films are smooth, compact and uniform. The structure and component of films were characterized using Raman and X-ray photoelectron spectroscopy, respectively. Friction coefficients of films were tested with ball-on-disk friction testing machine. The results show that the sp3 bond relative content decreases, however, carbon nitrogen and sp2 bond relative content increase in the films with increasing N2 cubic content in the working gas. Friction coefficients of the films decrease firstly, but increase subsequent with increasing N2 cubic content in the working gas. In order to achieve anti-frictional DLC films,the relative content of N2 in the working gas is as low as 20% in the present test.
    Keywords: 类金刚石膜 ; 非平衡磁控溅射 ; 摩擦特性 ; Diamond-Like Carbon Films ; Unbalance Magnetron Sputtering ; Friction Behaviors
    ISSN: 0254-0150
    Source: 维普数据 (Chongqing VIP Information Co.)
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