Document Open Access Logo

Specific Patterns Against Reference Sequences

Authors Marie-Pierre Béal , Maxime Crochemore

PDF

File

Thumbnail PDF
PDF
OASIcs.Grossi.14.pdf
  • Filesize: 0.77 MB
  • 12 pages

Document Identifiers

Subject Classification

ACM Subject Classification
  • Theory of computation → Regular languages
  • Theory of computation → Pattern matching
Keywords
  • Specific pattern
  • Minimal absent word
  • Minimal forbidden word
  • Directed Acyclic Word Graph (DAWG)
  • Suffix automaton

Metrics

  • Access Statistics
  • Total Accesses (updated on a weekly basis)
    0
    PDF Downloads
    0
    Metadata Views

Abstract

We design alignment-free techniques for comparing a set of sequences or just a word, called a target, against another set of words, called a reference. This is done with the detection of factor patterns that distinguish the target from the reference. A target-specific factor of a target T against a reference R is then a factor w of a word in T that is not a factor of a word in R but whose proper factors of w are factors of a word in R. The strategy is based on the notion of minimal absent/forbidden words.
We first address the computation of the set of target-specific factors of a target T against a reference R, where T and R are finite sets of sequences. The result is the construction of an automaton accepting the set of all considered target-specific factors. The construction algorithm runs in linear time according to the size of T ∪ R.
The second result is the design of an algorithm to compute all the occurrences in a single sequence T of its target-specific factors against a reference R. The algorithm runs in real-time on the target sequence, independently of the number of occurrences of target-specific factors.

Cite As Get BibTex

Marie-Pierre Béal and Maxime Crochemore. Specific Patterns Against Reference Sequences. In From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 132, pp. 14:1-14:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025) https://doi.org/10.4230/OASIcs.Grossi.14

Author Details

Marie-Pierre Béal
  • Univ. Gustave Eiffel, CNRS, LIGM, Champs-sur-Marne, France
Maxime Crochemore
  • Univ. Gustave Eiffel, CNRS, LIGM, Champs-sur-Marne, France
  • King’s College London, UK

References

  1. Lorraine A. K. Ayad, Golnaz Badkobeh, Gabriele Fici, Alice Héliou, and Solon P. Pissis. Constructing antidictionaries of long texts in output-sensitive space. Theory Comput. Syst., 65(5):777-797, 2021. URL: https://doi.org/10.1007/S00224-020-10018-5.
  2. Marie-Pierre Béal and Maxime Crochemore. Fast detection of specific fragments against a set of sequences. In 27th International Conference on Developments in Language Theory, DLT 2023, volume 13911 of Lecture Notes in Computer Science, pages 51-60, 2023. URL: https://doi.org/10.1007/978-3-031-33264-7_5.
  3. Marie-Pierre Béal, Maxime Crochemore, Filippo Mignosi, Antonio Restivo, and Marinella Sciortino. Computing forbidden words of regular languages. Fundam. Informaticae, 56(1-2):121-135, 2003. URL: http://content.iospress.com/articles/fundamenta-informaticae/fi56-1-2-08.
  4. Marie-Pierre Béal, Filippo Mignosi, Antonio Restivo, and Marinella Sciortino. Forbidden words in symbolic dynamics. Adv. Appl. Math., 25(2):163-193, 2000. URL: https://doi.org/10.1006/aama.2000.0682.
  5. G. Bernardini, C. Liu, G. Loukides, A. Marchetti-Spaccamela, S.P. Pissis, L. Stougie, and M. Sweering. Missing value replacement in strings and applications. Data Mining and Knowledge Discovery, 39(12), 2025. URL: https://doi.org/10.1007/s10618-024-01074-3.
  6. Giulia Bernardini, Alessio Conte, Garance Gourdel, Roberto Grossi, Grigorios Loukides, Nadia Pisanti, Solon P. Pissis, Giulia Punzi, Leen Stougie, and Michelle Sweering. Hide and Mine in Strings: Hardness, Algorithms, and Experiments . IEEE Transactions on Knowledge & Data Engineering, 35(06):5948-5963, June 2023. URL: https://doi.org/10.1109/TKDE.2022.3158063.
  7. A. Blumer, J. Blumer, D. Haussler, R. McConnell, and A. Ehrenfeucht. Complete inverted files for efficient text retrieval and analysis. Journal of the ACM, 34(3):578-595, 1987. URL: https://doi.org/10.1145/28869.28873.
  8. Anselm Blumer, J. Blumer, Andrzej Ehrenfeucht, David Haussler, and Ross M. McConnell. Building the minimal DFA for the set of all subwords of a word on-line in linear time. In Jan Paredaens, editor, Automata, Languages and Programming, 11th Colloquium, Antwerp, Belgium, July 16-20, 1984, Proceedings, volume 172 of Lecture Notes in Computer Science, pages 109-118. Springer, 1984. URL: https://doi.org/10.1007/3-540-13345-3_9.
  9. Paola Bonizzoni, Clelia De Felice, Yuri Pirola, Raffaella Rizzi, Rocco Zaccagnino, and Rosalba Zizza. Can formal languages help pangenomics to represent and analyze multiple genomes? In Volker Diekert and Mikhail V. Volkov, editors, Developments in Language Theory - 26th International Conference, DLT 2022, Tampa, FL, USA, May 9-13, 2022, Proceedings, volume 13257 of Lecture Notes in Computer Science, pages 3-12. Springer, 2022. URL: https://doi.org/10.1007/978-3-031-05578-2_1.
  10. Supaporn Chairungsee and Maxime Crochemore. Using minimal absent words to build phylogeny. Theor. Comput. Sci., 450:109-116, 2012. URL: https://doi.org/10.1016/J.TCS.2012.04.031.
  11. Panagiotis Charalampopoulos, Maxime Crochemore, Gabriele Fici, Robert Mercas, and Solon P. Pissis. Alignment-free sequence comparison using absent words. Inf. Comput., 262:57-68, 2018. URL: https://doi.org/10.1016/j.ic.2018.06.002.
  12. Maxime Crochemore. Transducers and repetitions. Theoretical Computer Science, 45(1):63-86, 1986. URL: https://doi.org/10.1016/0304-3975(86)90041-1.
  13. Maxime Crochemore. Longest common factor of two words. In Ehrig, Kowalski, Levi, and Montanari, editors, TAPSOFT'87 (Pisa, 1987), number 249 in LNCS, pages 26-36. Springer-Verlag, 1987. URL: https://doi.org/10.1007/3-540-17660-8_45.
  14. Maxime Crochemore, Christophe Hancart, and Thierry Lecroq. Algorithms on Strings. Cambridge University Press, 2007. 392 pages. Google Scholar
  15. Maxime Crochemore, Alice Héliou, Gregory Kucherov, Laurent Mouchard, Solon P. Pissis, and Yann Ramusat. Absent words in a sliding window with applications. Inf. Comput., 270, 2020. URL: https://doi.org/10.1016/j.ic.2019.104461.
  16. Maxime Crochemore, Filippo Mignosi, and Antonio Restivo. Automata and forbidden words. Inf. Process. Lett., 67(3):111-117, 1998. URL: https://doi.org/10.1016/S0020-0190(98)00104-5.
  17. Maxime Crochemore, Filippo Mignosi, Antonio Restivo, and Sergio Salemi. Data compression using antidictionaries. Proc. IEEE, 88(11):1756-1768, 2000. URL: https://doi.org/10.1109/5.892711.
  18. Paolo Ferragina and Giovanni Manzini. Opportunistic data structures with applications. In 41st Annual Symposium on Foundations of Computer Science, FOCS 2000, 12-14 November 2000, Redondo Beach, California, USA, pages 390-398. IEEE Computer Society, 2000. URL: https://doi.org/10.1109/SFCS.2000.892127.
  19. Yuta Fujishige, Yuki Tsujimaru, Shunsuke Inenaga, Hideo Bannai, and Masayuki Takeda. Computing dawgs and minimal absent words in linear time for integer alphabets. In Piotr Faliszewski, Anca Muscholl, and Rolf Niedermeier, editors, 41st International Symposium on Mathematical Foundations of Computer Science, MFCS 2016, August 22-26, 2016 - Kraków, Poland, volume 58 of LIPIcs, pages 38:1-38:14. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. URL: https://doi.org/10.4230/LIPICS.MFCS.2016.38.
  20. Yuta Fujishige, Yuki Tsujimaru, Shunsuke Inenaga, Hideo Bannai, and Masayuki Takeda. Linear-time computation of dawgs, symmetric indexing structures, and maws for integer alphabets. Theor. Comput. Sci., 973:114093, 2023. URL: https://doi.org/10.1016/J.TCS.2023.114093.
  21. Dan Gusfield. Algorithms on Strings, Trees, and Sequences - Computer Science and Computational Biology. Cambridge University Press, 1997. URL: https://doi.org/10.1017/cbo9780511574931.
  22. Christophe Hancart. On simon’s string searching algorithm. Inf. Process. Lett., 47(2):95-99, 1993. URL: https://doi.org/10.1016/0020-0190(93)90231-W.
  23. Parsoa Khorsand, Luca Denti, Human Genome Structural Variant Consortium, Paola Bonizzoni, Rayan Chikhi, and Fereydoun Hormozdiari. Comparative genome analysis using sample-specific string detection in accurate long reads. Bioinformatics Advances, 1(1), May 2021. URL: https://doi.org/10.1093/bioadv/vbab005.
  24. Donald E. Knuth, J. H. Morris Jr., and Vaughan R. Pratt. Fast pattern matching in strings. SIAM J. Comput., 6(2):323-350, 1977. URL: https://doi.org/10.1137/0206024.
  25. Heng Li. Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly. Bioinformatics, 28(14):1838-1844, May 2012. URL: https://doi.org/10.1093/bioinformatics/bts280.
  26. Udi Manber and Eugene W. Myers. Suffix arrays: A new method for on-line string searches. SIAM J. Comput., 22(5):935-948, 1993. URL: https://doi.org/10.1137/0222058.
  27. Filippo Mignosi, Antonio Restivo, and Marinella Sciortino. Forbidden factors in finite and infinite words. In Juhani Karhumäki, Hermann A. Maurer, Gheorghe Paun, and Grzegorz Rozenberg, editors, Jewels are Forever, Contributions on Theoretical Computer Science in Honor of Arto Salomaa, pages 339-350. Springer, 1999. Google Scholar
  28. Gonzalo Navarro and Mathieu Raffinot. Flexible pattern matching in strings - practical on-line search algorithms for texts and biological sequences. Cambridge University Press, 2002. 232 pages. URL: https://doi.org/10.1017/CBO9781316135228.
  29. Kouta Okabe, Takuya Mieno, Yuto Nakashima, Shunsuke Inenaga, and Hideo Bannai. Linear-time computation of generalized minimal absent words for multiple strings. In Franco Maria Nardini, Nadia Pisanti, and Rossano Venturini, editors, String Processing and Information Retrieval - 30th International Symposium, SPIRE 2023, Pisa, Italy, September 26-28, 2023, Proceedings, volume 14240 of Lecture Notes in Computer Science, pages 331-344. Springer, 2023. URL: https://doi.org/10.1007/978-3-031-43980-3_27.
  30. Armando J. Pinho, Paulo Jorge S. G. Ferreira, Sara P. Garcia, and João M. O. S. Rodrigues. On finding minimal absent words. BMC Bioinform., 10, 2009. URL: https://doi.org/10.1186/1471-2105-10-137.
  31. Diogo Pratas and Jorge M Silva. Persistent minimal sequences of sars-cov-2. Bioinformatics, 36(21):5129-5132, July 2020. URL: https://doi.org/10.1093/bioinformatics/btaa686.
  32. Mohammad Saifur Rahman, Ali Alatabbi, Tanver Athar, Maxime Crochemore, and M. Sohel Rahman. Absent words and the (dis)similarity analysis of dna sequences: an experimental study. BMC Research Notes, 9(186):1-8, 2016. URL: https://doi.org/10.1186/s13104-016-1972-z.
  33. Raquel M. Silva, Diogo Pratas, Luísa Castro, Armando J. Pinho, and Paulo Jorge S. G. Ferreira. Three minimal sequences found in ebola virus genomes and absent from human DNA. Bioinform., 31(15):2421-2425, 2015. URL: https://doi.org/10.1093/bioinformatics/btv189.
  34. Imre Simon. String matching algorithms and automata. In Juhani Karhumäki, Hermann A. Maurer, and Grzegorz Rozenberg, editors, Results and Trends in Theoretical Computer Science, Colloquium in Honor of Arto Salomaa, Graz, Austria, June 10-11, 1994, Proceedings, volume 812 of Lecture Notes in Computer Science, pages 386-395. Springer, 1994. URL: https://doi.org/10.1007/3-540-58131-6_61.
Questions / Remarks / Feedback
X

Feedback for Dagstuhl Publishing


Thanks for your feedback!

Feedback submitted

Could not send message

Please try again later or send an E-mail
© 2023-2025 Schloss Dagstuhl – LZI GmbH About DROPS Imprint Privacy Contact