Run-Length Compressed Indexes Are Superior for Highly Repetitive Sequence Collections

Näytä kaikki kuvailutiedot

Permalink

http://hdl.handle.net/10138/1200

Lähdeviite

In Proc. 15th Symposium on String Processing and Information Retrieval, LNCS 5280, pp. 164–175, 2008.

Julkaisun nimi: Run-Length Compressed Indexes Are Superior for Highly Repetitive Sequence Collections
Tekijä: Siren, Jouni; Välimäki, Niko; Mäkinen, Veli; Navarro, Gonzalo
Tiivistelmä: 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. This paper is devoted to studying ways to store massive sets of highly repetitive sequence collections in space-efficient manner so that retrieval of the content as well as queries on the content of the sequences can be provided time-efficiently. We show that the state-of-the-art entropy-bound full-text self-indexes do not yet provide satisfactory space bounds for this specific task. We engineer some new structures that use run-length encoding and give empirical evidence that these structures are superior to the current structures.
URI: http://hdl.handle.net/10138/1200
Päiväys: 2008


Tiedostot

Latausmäärä yhteensä: Ladataan...

Tiedosto(t) Koko Formaatti Näytä
paper.pdf 173.7KB PDF Avaa tiedosto

Viite kuuluu kokoelmiin:

Näytä kaikki kuvailutiedot