Storage and retrieval of individual genomes

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http://hdl.handle.net/10138/23701

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Mäkinen , V , Navarro , G , Sirén , J & Välimäki , N 2009 , ' Storage and retrieval of individual genomes ' in Research in Computational Molecular Biology : 13th Annual International Conference, RECOMB 2009 , pp. 121-137 Lecture Notes in Computer Science , no. 5541 . DOI: 10.1007/978-3-642-02008-7_9

Title: Storage and retrieval of individual genomes
Author: Mäkinen, Veli; Navarro, Gonzalo; Sirén, Jouni; Välimäki, Niko
Contributor: University of Helsinki, Department of Computer Science (-2009)
University of Helsinki, Department of Computer Science (-2009)
University of Helsinki, Department of Computer Science (-2009)
Belongs to series: Lecture Notes in Computer Science
Belongs to series: Research in Computational Molecular Biology 13th Annual International Conference, RECOMB 2009
Abstract: A repetitive sequence collection is one where portions of a base sequence of length n are repeated many times with small variations, forming a collection of total length N. Examples of such collections are version control data and genome sequences of individuals, where the differences can be expressed by lists of basic edit operations. Flexible and efficient data analysis on a such typically huge collection is plausible using suffix trees. However, suffix tree occupies O(N log N) bits, which very soon inhibits in-memory analyses. Recent advances in full-text self-indexing reduce the space of suffix tree to O(N log σ) bits, where σ is the alphabet size. In practice, the space reduction is more than 10-fold, for example on suffix tree of Human Genome. However, this reduction factor remains constant when more sequences are added to the collection. We develop a new family of self-indexes suited for the repetitive sequence collection setting. Their expected space requirement depends only on the length n of the base sequence and the number s of variations in its repeated copies. That is, the space reduction factor is no longer constant, but depends on N / n. We believe the structures developed in this work will provide a fundamental basis for storage and retrieval of individual genomes as they become available due to rapid progress in the sequencing technologies.
Peer review status: Peer reviewed
URI: http://hdl.handle.net/10138/23701
Date: 2009
Subject: 113 Computer and information sciences
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