Storage and retrieval of individual genomes

Veli Mäkinen, Gonzalo Navarro, Jouni Sirén, Niko Välimäki

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review

Sammanfattning

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.
Originalspråkengelska
Titel på gästpublikationResearch in Computational Molecular Biology : 13th Annual International Conference, RECOMB 2009
RedaktörerSerafim Batzoglou
Antal sidor17
FörlagSpringer
Utgivningsdatum2009
Sidor121-137
ISBN (tryckt)978-3-642-02007-0
DOI
StatusPublicerad - 2009
MoE-publikationstypA4 Artikel i en konferenspublikation
EvenemangAnnual International Conference on Research in Computational Molecular Biology - Tucson, Arizona, Förenta Staterna (USA)
Varaktighet: 18 maj 200921 maj 2009
Konferensnummer: 13

Publikationsserier

NamnLecture Notes in Computer Science
Nummer5541

Vetenskapsgrenar

  • 113 Data- och informationsvetenskap

Citera det här

Mäkinen, V., Navarro, G., Sirén, J., & Välimäki, N. (2009). Storage and retrieval of individual genomes. I S. Batzoglou (Red.), Research in Computational Molecular Biology: 13th Annual International Conference, RECOMB 2009 (s. 121-137). (Lecture Notes in Computer Science; Nr. 5541). Springer. https://doi.org/10.1007/978-3-642-02008-7_9
Mäkinen, Veli ; Navarro, Gonzalo ; Sirén, Jouni ; Välimäki, Niko. / Storage and retrieval of individual genomes. Research in Computational Molecular Biology: 13th Annual International Conference, RECOMB 2009. redaktör / Serafim Batzoglou. Springer, 2009. s. 121-137 (Lecture Notes in Computer Science; 5541).
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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.",
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Mäkinen, V, Navarro, G, Sirén, J & Välimäki, N 2009, Storage and retrieval of individual genomes. i S Batzoglou (red.), Research in Computational Molecular Biology: 13th Annual International Conference, RECOMB 2009. Lecture Notes in Computer Science, nr. 5541, Springer, s. 121-137, Annual International Conference on Research in Computational Molecular Biology, Tucson, Arizona, Förenta Staterna (USA), 18/05/2009. https://doi.org/10.1007/978-3-642-02008-7_9

Storage and retrieval of individual genomes. / Mäkinen, Veli; Navarro, Gonzalo; Sirén, Jouni; Välimäki, Niko.

Research in Computational Molecular Biology: 13th Annual International Conference, RECOMB 2009. red. / Serafim Batzoglou. Springer, 2009. s. 121-137 (Lecture Notes in Computer Science; Nr. 5541).

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review

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T1 - Storage and retrieval of individual genomes

AU - Mäkinen, Veli

AU - Navarro, Gonzalo

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N2 - 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.

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Mäkinen V, Navarro G, Sirén J, Välimäki N. Storage and retrieval of individual genomes. I Batzoglou S, redaktör, Research in Computational Molecular Biology: 13th Annual International Conference, RECOMB 2009. Springer. 2009. s. 121-137. (Lecture Notes in Computer Science; 5541). https://doi.org/10.1007/978-3-642-02008-7_9