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WorldCIST'19 - 7th World Conference on Information Systems and Technologies

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ND-GiST: A novel method for disk-resident k-mer indexing

Several challenges are related to metagenomics, one of which is the data management. A related central concept is k-mer which means a possible subsequence of length k from a DNA (sub)sequence. In this work, the focus is on indexing k-mers and supporting box queries where a query string of length k might have multiple allowed nucleobases per position. A novel index structure: ND-GiST is introduced which has capability to handle box queries. Comparing it with full table scan and the traditional B-tree, the performance results of ND-GiST are encouraging.

János Szalai-Gindl
Department of Information Systems, Eötvös Loránd University
Hungary

Attila Kiss
Department of Information Systems, Eötvös Loránd University
Hungary

Gábor Halász
Department of Information Systems, Eötvös Loránd University
Hungary

László Dobos
Department of Physics of Complex Systems, Eötvös Loránd University
Hungary

István Csabai
Department of Physics of Complex Systems, Eötvös Loránd University
Hungary

 


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