Suffix Tree of Alignment: An Efficient Index for Similar Data

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68407700%3A21240%2F13%3A00209113" target="_blank" >RIV/68407700:21240/13:00209113 - isvavai.cz</a>

Výsledek na webu

<a href="http://link.springer.com/chapter/10.1007/978-3-642-45278-9_29" target="_blank" >http://link.springer.com/chapter/10.1007/978-3-642-45278-9_29</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1007/978-3-642-45278-9_29" target="_blank" >10.1007/978-3-642-45278-9_29</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Suffix Tree of Alignment: An Efficient Index for Similar Data

Popis výsledku v původním jazyce

We consider an index data structure for similar strings. The generalized suffix tree can be a solution for this. The generalized suffix tree of two strings A and B is a compacted trie representing all suffixes in A and B. It has |A|+|B| leaves and can beconstructed in O(|A|+|B|) time. However, if the two strings are similar, the generalized suffix tree is not efficient because it does not exploit the similarity which is usually represented as an alignment of A and B. In this paper we propose a space/time-efficient suffix tree of alignment which wisely exploits the similarity in an alignment. Our suffix tree for an alignment of A and B has |A|+ld +l1 leaves where ld is the sum of the lengths of all parts of B different from A and l1 is the sum of the lengths of some common parts of A and B. We did not compromise the pattern search to reduce the space. Our suffix tree can be searched for a pattern P in O(|P | + occ) time where occ is the number of occurrences of P in A and B. We also pr

Název v anglickém jazyce

Suffix Tree of Alignment: An Efficient Index for Similar Data

Popis výsledku anglicky

We consider an index data structure for similar strings. The generalized suffix tree can be a solution for this. The generalized suffix tree of two strings A and B is a compacted trie representing all suffixes in A and B. It has |A|+|B| leaves and can beconstructed in O(|A|+|B|) time. However, if the two strings are similar, the generalized suffix tree is not efficient because it does not exploit the similarity which is usually represented as an alignment of A and B. In this paper we propose a space/time-efficient suffix tree of alignment which wisely exploits the similarity in an alignment. Our suffix tree for an alignment of A and B has |A|+ld +l1 leaves where ld is the sum of the lengths of all parts of B different from A and l1 is the sum of the lengths of some common parts of A and B. We did not compromise the pattern search to reduce the space. Our suffix tree can be searched for a pattern P in O(|P | + occ) time where occ is the number of occurrences of P in A and B. We also pr

Druh

D - Stať ve sborníku

CEP obor

IN - Informatika

OECD FORD obor

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Projekt

<a href="/cs/project/GA13-03253S" target="_blank" >GA13-03253S: Zpracování textových a stromových struktur a jejich aplikace</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2013

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název statě ve sborníku

Proceedings of the 24th Workshop on Combinatorial Algorithms (IWOCA 2013)

ISBN

978-3-642-45277-2

ISSN

0302-9743

e-ISSN

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Počet stran výsledku

12

Strana od-do

337-348

Název nakladatele

Springer

Místo vydání

Berlin

Místo konání akce

Rouen

Datum konání akce

10. 7. 2013

Typ akce podle státní příslušnosti

WRD - Celosvětová akce

Kód UT WoS článku

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