Suffix tree of alignment: An efficient index for similar data
DC Field | Value | Language |
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dc.contributor.author | Na, Joong Chae | - |
dc.contributor.author | Park, Heejin | - |
dc.contributor.author | Crochemore, Maxime | - |
dc.contributor.author | Holub, Jan | - |
dc.contributor.author | Iliopoulos, Costas S. | - |
dc.contributor.author | Mouchard, Laurent | - |
dc.contributor.author | Park, Kunsoo | - |
dc.date.accessioned | 2022-07-16T09:07:29Z | - |
dc.date.available | 2022-07-16T09:07:29Z | - |
dc.date.created | 2021-05-13 | - |
dc.date.issued | 2013-07 | - |
dc.identifier.issn | 0302-9743 | - |
dc.identifier.uri | https://scholarworks.bwise.kr/hanyang/handle/2021.sw.hanyang/162359 | - |
dc.description.abstract | 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 be constructed 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| + l d + l 1 leaves where l d is the sum of the lengths of all parts of B different from A and l 1 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 present an efficient algorithm to construct the suffix tree of alignment. When the suffix tree is constructed from scratch, the algorithm requires O(|A| + l d + l 1 + l 2) time where l 2 is the sum of the lengths of other common substrings of A and B. When the suffix tree of A is already given, it requires O(l d + l 1 + l 2) time. | - |
dc.language | 영어 | - |
dc.language.iso | en | - |
dc.publisher | Springer Verlag | - |
dc.title | Suffix tree of alignment: An efficient index for similar data | - |
dc.type | Article | - |
dc.contributor.affiliatedAuthor | Park, Heejin | - |
dc.identifier.doi | 10.1007/978-3-642-45278-9_29 | - |
dc.identifier.scopusid | 2-s2.0-84893109534 | - |
dc.identifier.bibliographicCitation | Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), v.8288 LNCS, pp.337 - 348 | - |
dc.relation.isPartOf | Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | - |
dc.citation.title | Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | - |
dc.citation.volume | 8288 LNCS | - |
dc.citation.startPage | 337 | - |
dc.citation.endPage | 348 | - |
dc.type.rims | ART | - |
dc.type.docType | Conference Paper | - |
dc.description.journalClass | 1 | - |
dc.description.isOpenAccess | N | - |
dc.description.journalRegisteredClass | scopus | - |
dc.subject.keywordPlus | Index data structures | - |
dc.subject.keywordPlus | Pattern search | - |
dc.subject.keywordPlus | Similar datum | - |
dc.subject.keywordPlus | Sub-strings | - |
dc.subject.keywordPlus | Suffix-trees | - |
dc.subject.keywordPlus | Algorithms | - |
dc.subject.keywordPlus | Alignment | - |
dc.subject.keywordPlus | Combinatorial mathematics | - |
dc.subject.keywordPlus | Forestry | - |
dc.subject.keywordPlus | Trees (mathematics) | - |
dc.subject.keywordPlus | Algorithms | - |
dc.subject.keywordPlus | Forestry | - |
dc.subject.keywordPlus | Mathematics | - |
dc.subject.keywordPlus | Trees | - |
dc.subject.keywordAuthor | alignments | - |
dc.subject.keywordAuthor | Indexes for similar data | - |
dc.subject.keywordAuthor | suffix trees | - |
dc.identifier.url | https://link.springer.com/chapter/10.1007/978-3-642-45278-9_29 | - |
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