Browsing by Subject "Hash table"

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    Accelerating read mapping with FastHASH
    (BioMed Central Ltd., 2013) Xin, H.; Lee, D.; Hormozdiari, F.; Yedkar, S.; Mutlu, O.; Alkan C.
    With the introduction of next-generation sequencing (NGS) technologies, we are facing an exponential increase in the amount of genomic sequence data. The success of all medical and genetic applications of next-generation sequencing critically depends on the existence of computational techniques that can process and analyze the enormous amount of sequence data quickly and accurately. Unfortunately, the current read mapping algorithms have difficulties in coping with the massive amounts of data generated by NGS. We propose a new algorithm, FastHASH, which drastically improves the performance of the seed-and-extend type hash table based read mapping algorithms, while maintaining the high sensitivity and comprehensiveness of such methods. FastHASH is a generic algorithm compatible with all seed-and-extend class read mapping algorithms. It introduces two main techniques, namely Adjacency Filtering, and Cheap K-mer Selection. We implemented FastHASH and merged it into the codebase of the popular read mapping program, mrFAST. Depending on the edit distance cutoffs, we observed up to 19-fold speedup while still maintaining 100% sensitivity and high comprehensiveness. © 2013 Xin et al.
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    Characterizing Gnutella network properties for peer-to-peer network simulation
    (Springer, Berlin, Heidelberg, 2005) Çıracı, Selim; Körpeoğlu, İbrahim; Ulusoy, Özgür
    A P2P network that is overlayed over Internet can consist of thousands, or even millions of nodes. To analyze the performance of a P2P network, or an algorithm or protocol designed for a P2P network, simulation studies have to be performed quite often, and simulation studies require the use of appropriate models for various components and parameters of a P2P network simulated. Therefore it is important to have models and statistical information about various parameters and properties of a P2P network. This paper tries to model and obtain the characteristics of some of the important parameters of one widely used P2P network, Gnutella. The methodology to derive the characteristics is based on collecting P2P protocol traces from the Gnutella network that is currently running over the Internet, and analyzing the collected traces. The results we present in this paper will be an important ingredient for studies that are based on simulation of P2P networks, especially unstructured P2P networks. © Springer-Verlag Berlin Heidelberg 2005.