| 1 |
Hierarchical Overlap Graph
|
|
|
|
In: ISSN: 0020-0190 ; Information Processing Letters ; https://hal-lirmm.ccsd.cnrs.fr/lirmm-01674319 ; Information Processing Letters, Elsevier, 2020, 155, pp.#105862. ⟨10.1016/j.ipl.2019.105862⟩ (2020)
|
|
BASE
|
|
Show details
|
|
|
| 2 |
Full Compressed Affix Tree Representations
|
|
|
|
In: IEEE Data Compression Conference ; DCC: Data Compression Conference ; https://hal-lirmm.ccsd.cnrs.fr/lirmm-02093302 ; DCC: Data Compression Conference, IEEE, Apr 2017, Snowbird, UT, United States. pp.102-111, ⟨10.1109/DCC.2017.39⟩ ; http://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=7921793 (2017)
|
|
BASE
|
|
Show details
|
|
|
| 3 |
Construction of a de Bruijn Graph for Assembly from a Truncated Suffix Tree
|
|
|
|
In: 9th International Conference on Language and Automata Theory and Applications ; LATA: Language and Automata Theory and Applications ; https://hal.archives-ouvertes.fr/hal-01955978 ; LATA: Language and Automata Theory and Applications, Mar 2015, Nice, France. pp.109-120, ⟨10.1007/978-3-319-15579-1_8⟩ ; http://grammars.grlmc.com/LATA2015/ (2015)
|
|
BASE
|
|
Show details
|
|
|
| 4 |
Reverse engineering of compact suffix trees and links: A novel algorithm
|
|
|
|
In: ISSN: 1570-8667 ; Journal of Discrete Algorithms ; https://hal-lirmm.ccsd.cnrs.fr/lirmm-01082098 ; Journal of Discrete Algorithms, Elsevier, 2014, StringMasters 2012 & 2013 Special Issue (Volume 1), 28, pp.9-22. ⟨10.1016/j.jda.2014.07.002⟩ (2014)
|
|
Abstract:
Edited by Maxime Crochemore, Jacqueline W. Daykin and Zsuzsanna Lipták ; International audience ; Invented in the 70's, the Suffix Tree (ST) is a data structure that indexes all substrings of a text in linear space. Although more space demanding than other indexes, the ST remains an inspiring index likely because it represents substrings in a hierarchical tree structure. Along time, STs have acquired a central position in text algorithmics with myriad of algorithms and applications to for instance motif discovery, biological sequence comparison, or text compres-sion. It is well known that different words can lead to the same suffix tree structure with different labels. Moreover, the properties of STs prevent all tree structures from being STs. Even the suffix links, which play a key role in efficient construction algorithms and many ap-plications, are not sufficient to discriminate the suffix trees of distinct words. The question of recognising which trees can be STs has been raised and termed Reverse Engineering on STs. For the case where a tree is given with potential suffix links, a seminal work provides a linear time solution only for binary alphabets. Here, we also investigate the Reverse Engineering problem on ST with links and exhibit a novel approach and algorithm. Hopefully, this new suffix tree characterisation makes up a valuable step towards a better understanding of suffix tree combinatorics. * This work is supported by ANR Colib'read (ANR-12-BS02-0008) and Défi MASTODONS SePhHaDe from CNRS.
|
|
Keyword:
[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]; [INFO.INFO-DS]Computer Science [cs]/Data Structures and Algorithms [cs.DS]; [INFO]Computer Science [cs]; characterisation; combinatorics; connectivity; data structures; Eulerian tour; graph; index; permutation; recognition; stringology; suffix tree; text indexing
|
|
URL: https://hal-lirmm.ccsd.cnrs.fr/lirmm-01082098
https://hal-lirmm.ccsd.cnrs.fr/lirmm-01082098/file/Cazaux-Rivals-JDA-encrypt.pdf
https://doi.org/10.1016/j.jda.2014.07.002
https://hal-lirmm.ccsd.cnrs.fr/lirmm-01082098/document
|
|
BASE
|
|
Hide details
|
|
|
|
|
