Prospects and limitations of full-text index structures in genome analysis
Identifieur interne : 000750 ( Main/Merge ); précédent : 000749; suivant : 000751Prospects and limitations of full-text index structures in genome analysis
Auteurs : Michaël Vyverman ; Bernard De Baets [Belgique] ; Veerle Fack ; Peter DawyndtSource :
- Nucleic Acids Research [ 0305-1048 ] ; 2012.
Abstract
The combination of incessant advances in sequencing technology producing large amounts of data and innovative bioinformatics approaches, designed to cope with this data flood, has led to new interesting results in the life sciences. Given the magnitude of sequence data to be processed, many bioinformatics tools rely on efficient solutions to a variety of complex string problems. These solutions include fast heuristic algorithms and advanced data structures, generally referred to as index structures. Although the importance of index structures is generally known to the bioinformatics community, the design and potency of these data structures, as well as their properties and limitations, are less understood. Moreover, the last decade has seen a boom in the number of variant index structures featuring complex and diverse memory-time trade-offs. This article brings a comprehensive state-of-the-art overview of the most popular index structures and their recently developed variants. Their features, interrelationships, the trade-offs they impose, but also their practical limitations, are explained and compared.
Url:
DOI: 10.1093/nar/gks408
PubMed: 22584621
PubMed Central: 3424560
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Vyverman</name><affiliation><nlm:aff wicri:cut=" and" id="gks408-AFF1">Department of Applied Mathematics and Computer Science, Ghent University, Building S9, 281 Krijgslaan</nlm:aff><wicri:noCountry code="subfield">281 Krijgslaan</wicri:noCountry></affiliation></author><author><name sortKey="De Baets, Bernard" sort="De Baets, Bernard" uniqKey="De Baets B" first="Bernard" last="De Baets">Bernard De Baets</name><affiliation wicri:level="1"><nlm:aff id="gks408-AFF1">Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, 653 Coupure links, Ghent, B-9000, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, 653 Coupure links, Ghent, B-9000</wicri:regionArea><wicri:noRegion>B-9000</wicri:noRegion></affiliation></author><author><name sortKey="Fack, Veerle" sort="Fack, Veerle" uniqKey="Fack V" first="Veerle" last="Fack">Veerle Fack</name><affiliation><nlm:aff wicri:cut=" and" id="gks408-AFF1">Department of Applied Mathematics and Computer Science, Ghent University, Building S9, 281 Krijgslaan</nlm:aff><wicri:noCountry code="subfield">281 Krijgslaan</wicri:noCountry></affiliation></author><author><name sortKey="Dawyndt, Peter" sort="Dawyndt, Peter" uniqKey="Dawyndt P" first="Peter" last="Dawyndt">Peter Dawyndt</name><affiliation><nlm:aff wicri:cut=" and" id="gks408-AFF1">Department of Applied Mathematics and Computer Science, Ghent University, Building S9, 281 Krijgslaan</nlm:aff><wicri:noCountry code="subfield">281 Krijgslaan</wicri:noCountry></affiliation></author></analytic><series><title level="j">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The combination of incessant advances in sequencing technology producing large amounts of data and innovative bioinformatics approaches, designed to cope with this data flood, has led to new interesting results in the life sciences. Given the magnitude of sequence data to be processed, many bioinformatics tools rely on efficient solutions to a variety of complex string problems. These solutions include fast heuristic algorithms and advanced data structures, generally referred to as index structures. Although the importance of index structures is generally known to the bioinformatics community, the design and potency of these data structures, as well as their properties and limitations, are less understood. Moreover, the last decade has seen a boom in the number of variant index structures featuring complex and diverse memory-time trade-offs. This article brings a comprehensive state-of-the-art overview of the most popular index structures and their recently developed variants. Their features, interrelationships, the trade-offs they impose, but also their practical limitations, are explained and compared.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Felsenstein, J" uniqKey="Felsenstein J">J Felsenstein</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ferragina, P" uniqKey="Ferragina P">P Ferragina</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Altschul, S" uniqKey="Altschul S">S Altschul</name></author><author><name sortKey="Gish, W" uniqKey="Gish W">W Gish</name></author><author><name sortKey="Miller, W" uniqKey="Miller W">W Miller</name></author><author><name sortKey="Myers, E" uniqKey="Myers E">E Myers</name></author><author><name sortKey="And Lipman, D" uniqKey="And Lipman D">D and Lipman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Flicek, P" uniqKey="Flicek P">P 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sortKey="Salson, M" uniqKey="Salson M">M Salson</name></author><author><name sortKey="Lecroq, T" uniqKey="Lecroq T">T Lecroq</name></author><author><name sortKey="Leonard, M" uniqKey="Leonard M">M Léonard</name></author><author><name sortKey="Mouchard, L" uniqKey="Mouchard L">L Mouchard</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="M Kinen, V" uniqKey="M Kinen V">V Mäkinen</name></author><author><name sortKey="Navarro, G" uniqKey="Navarro G">G Navarro</name></author><author><name sortKey="Siren, J" uniqKey="Siren J">J Sirén</name></author><author><name sortKey="V Lim Ki, N" uniqKey="V Lim Ki N">N Välimäki</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kuruppu, S" uniqKey="Kuruppu S">S Kuruppu</name></author><author><name sortKey="Puglisi, S" uniqKey="Puglisi S">S Puglisi</name></author><author><name sortKey="Zobel, J" uniqKey="Zobel J">J 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