Výsledky vyhledávání - "Degenerate string"

Akademický článek

Autor: Esteban Gabory, Moses Njagi Mwaniki, Nadia Pisanti, Solon P. Pissis, Jakub Radoszewski, Michelle Sweering, Wiktor Zuba

Publikováno v: Frontiers in Bioinformatics, Vol 4 (2024)

IntroductionAn elastic-degenerate (ED) string is a sequence of sets of strings. It can also be seen as a directed acyclic graph whose edges are labeled by strings. The notion of ED strings was introduced as a simple alternative to variation and seque

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Akademický článek

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ELASTIC-DEGENERATE STRING MATCHING VIA FAST MATRIX MULTIPLICATION

Autor: Giulia Bernardini, Paweł Gawrychowski, Nadia Pisanti, Solon P. Pissis, Giovanna Rosone

Publikováno v: SIAM Journal on Computing
SIAM Journal on Computing, 2022, 51 (3), pp.549-576. ⟨10.1137/20M1368033⟩
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Bernardini, G, Gawrychowski, P, Pisanti, N, Pissis, S P & Rosone, G 2022, ' ELASTIC-DEGENERATE STRING MATCHING VIA FAST MATRIX MULTIPLICATION ', SIAM Journal on Computing, vol. 51, no. 3, pp. 549-576 . https://doi.org/10.1137/20M1368033
SIAM Journal on Computing, 51(3), 549-576
SIAM Journal on Computing, 51(3), 549-576. Society for Industrial and Applied Mathematics Publications
Bernardini, G, Gawrychowski, P, Pisanti, N, Pissis, S P & Rosone, G 2022, ' Elastic-Degenerate String Matching via Fast Matrix Multiplication ', SIAM Journal on Computing, vol. 51, no. 3, pp. 549-576 . https://doi.org/10.1137/20M1368033

An elastic-degenerate (ED) string is a sequence of $n$ sets of strings of total length $N$, which was recently proposed to model a set of similar sequences. The ED string matching (EDSM) problem is to find all occurrences of a pattern of length $m$ i

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e05b6ad51675d74ee543feddedca5fc3
https://ir.cwi.nl/pub/32732

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Comparing Elastic-Degenerate Strings: Algorithms, Lower Bounds, and Applications

Autor: Gabory, Esteban, Mwaniki, Moses Njagi, Pisanti, Nadia, Pissis, Solon P., Radoszewski, Jakub, Sweering, Michelle, Zuba, Wiktor

An elastic-degenerate (ED) string T is a sequence of n sets T[1],…,T[n] containing m strings in total whose cumulative length is N. We call n, m, and N the length, the cardinality and the size of T, respectively. The language of T is defined as ℒ

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Conference

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Elastic-Degenerate String Matching with 1 Error

Autor: Bernardini, Giulia, Gabory, Esteban, Pissis, Solon P., Stougie, Leen, Sweering, Michelle, Zuba, Wiktor, Castañeda, Armando, Rodríguez-Henríquez, Francisco

Publikováno v: LATIN 2022: Theoretical Informatics
LATIN 2022: Theoretical Informatics, 2022, Guanajuato, Mexico. pp.20-37, ⟨10.1007/978-3-031-20624-5_2⟩
LATIN 2022: Theoretical Informatics: 15th Latin American Symposium, Guanajuato, Mexico, November 7–11, 2022, Proceedings, 20-37
STARTPAGE=20;ENDPAGE=37;TITLE=LATIN 2022: Theoretical Informatics
LATIN 2022: Theoretical Informatics ISBN: 9783031206238
Bernardini, G, Gabory, E, Pissis, S P, Stougie, L, Sweering, M & Zuba, W 2022, Elastic-Degenerate String Matching with 1 Error . in A Castañeda & F Rodríguez-Henríquez (eds), LATIN 2022: Theoretical Informatics : 15th Latin American Symposium, Guanajuato, Mexico, November 7–11, 2022, Proceedings . Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 13568 LNCS, Springer Science and Business Media Deutschland GmbH, pp. 20-37, 15th Latin American Symposium on Theoretical Informatics, LATIN 2022, Guanajuato, Mexico, 7/11/22 . https://doi.org/10.1007/978-3-031-20624-5_2
Lecture Notes in Computer Science
Lecture Notes in Computer Science-LATIN 2022: Theoretical Informatics

An elastic-degenerate string is a sequence of $n$ finite sets of strings of total length $N$, introduced to represent a set of related DNA sequences, also known as a pangenome. The ED string matching (EDSM) problem consists in reporting all occurrenc

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6a2dd1f39e375832de43549cb4def4d5
https://inria.hal.science/hal-03913707/file/2209.01095.pdf

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Comparing Degenerate Strings

Autor: Giulia Bernardini, Nadia Pisanti, Solon P. Pissis, Lorraine A.K. Ayad, Roberto Grossi, Giovanna Rosone, Mai Alzamel, Costas S. Iliopoulos

Publikováno v: Fundamenta Informaticae, 175(1-4), 41-58
Fundamenta Informaticae
Fundamenta Informaticae, 2020, 175, pp.41-58. ⟨10.3233/fi-2020-1947⟩
Fundamenta Informaticae, Polskie Towarzystwo Matematyczne, 2020, 175, pp.41-58. ⟨10.3233/fi-2020-1947⟩

Uncertain sequences are compact representations of sets of similar strings. They highlight common segments by collapsing them, and explicitly represent varying segments by listing all possible options. A generalized degenerate string (GD string) is a

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8f875ebb0f9720a2bdd77d492626bcd4
http://hdl.handle.net/11368/3019828

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On-Line Pattern Matching on D-Texts (Invited Talk)

Autor: Pisanti, Nadia

The Elastic Degenerate String Matching (EDSM) problem is defined as that of finding an occurrence of a pattern P of length m in an ED-text T. A D-text (Degenerate text) is a string that actually represents a set of similar and aligned strings (e.g. a

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::780a96629f200ae130ab3d66a59e4a6c
http://hdl.handle.net/11568/1120069

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Approximate pattern matching on elastic-degenerate text

Autor: Solon P. Pissis, Giovanna Rosone, Giulia Bernardini, Nadia Pisanti

Publikováno v: Theoretical Computer Science
Theoretical Computer Science, Elsevier, 2019, pp.1-30. ⟨10.1016/j.tcs.2019.08.012⟩
Theoretical Computer Science, 812, 109-122
Theoretical Computer Science, 2019, pp.1-30. ⟨10.1016/j.tcs.2019.08.012⟩

An elastic-degenerate string is a sequence of n sets of strings of total length N. It has been introduced to represent a multiple alignment of several closely-related sequences (e.g., pan-genome) compactly. In this representation, substrings of these

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a670d1a538614c53812c912424114b13
https://hal.inria.fr/hal-02298622/document

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Even Faster Elastic-Degenerate String Matching via Fast Matrix Multiplication

Autor: Bernardini, Giulia, Gawrychowski, Paweł, Pisanti, Nadia, Pissis, Solon, Rosone, Giovanna

Publikováno v: ICALP 2019-46th International Colloquium on Automata, Languages and Programming
ICALP 2019-46th International Colloquium on Automata, Languages and Programming, Jul 2019, Patras, Greece. pp.1-15, ⟨10.4230/LIPIcs.ICALP.2019.21⟩

An elastic-degenerate (ED) string is a sequence of n sets of strings of total length N, which was recently proposed to model a set of similar sequences. The ED string matching (EDSM) problem is to find all occurrences of a pattern of length m in an E

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ec6d1aec2a5edb1ff95d049890843404
http://hdl.handle.net/11568/995182

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