K. Abrahamson, Generalized string matching, SIAM J. Comput, vol.16, issue.6, pp.1039-1051, 1987.

M. Adamczyk, M. Alzamel, P. Charalampopoulos, C. S. Iliopoulos, and J. Radoszewski, Palindromic decompositions with gaps and errors, CSR, vol.10304, pp.48-61, 2017.
DOI : 10.1007/978-3-319-58747-9_7

URL : http://arxiv.org/pdf/1703.08931

A. Alatabbi, S. Costas, M. Iliopoulos, and . Sohel-rahman, Maximal palindromic factorization, PSC, pp.70-77, 2013.

Y. Almirantis, P. Charalampopoulos, J. Gao, S. Costas, and . Iliopoulos, On avoided words, absent words, and their application to biological sequence analysis, Algorithms for Molecular Biology, vol.12, issue.1, p.5, 2017.
DOI : 10.1186/s13015-017-0094-z

URL : https://doi.org/10.1186/s13015-017-0094-z

M. Alzamel, J. Gao, C. S. Iliopoulos, C. Liu, and S. P. Pissis, Efficient computation of palindromes in sequences with uncertainties, EANN, vol.744, pp.620-629, 2017.

A. Apostolico, D. Breslauer, and Z. Galil, Parallel detection of all palindromes in a string, Theoretical Computer Science, vol.141, issue.1, pp.163-173, 1995.

A. Michael, M. Bender, and . Farach-colton, The LCA problem revisited, LATIN, volume 1776 of LNCS, pp.88-94, 2000.

G. Bernardini, N. Pisanti, P. Solon, G. Pissis, and . Rosone, Pattern matching on elastic-degenerate text with errors, SPIRE, volume 10508 of LNCS, pp.74-90, 2017.
DOI : 10.1007/978-3-319-67428-5_7

URL : https://hal.archives-ouvertes.fr/hal-01673585

K. Borozdin, D. Kosolobov, M. Rubinchik, and A. M. Shur, Palindromic Length in Linear Time, 12. Schloss DagstuhlLeibniz-Zentrum fuer Informatik, vol.23, pp.1-23, 2017.

, The Computational Pan-Genomics Consortium. Computational pan-genomics: status, promises and challenges, Briefings in Bioinformatics, vol.21, p.13, 2016.

M. Crochemore, S. Costas, T. Iliopoulos, J. Kociumaka, W. Radoszewski et al., Covering problems for partial words and for indeterminate strings, Theoretical Computer Science, vol.698, pp.25-39, 2017.
DOI : 10.1016/j.tcs.2017.05.026

URL : http://arxiv.org/pdf/1412.3696

M. Farach, Optimal suffix tree construction with large alphabets, FOCS, pp.137-143, 1997.
DOI : 10.1109/sfcs.1997.646102

G. Fici, T. Gagie, J. Kärkkäinen, and D. Kempa, A subquadratic algorithm for minimum palindromic factorization, Journal of Discrete Algorithms, vol.28, pp.41-48, 2014.
DOI : 10.1016/j.jda.2014.08.001

URL : https://doi.org/10.1016/j.jda.2014.08.001

C. Martin, U. Frith, J. L. Hansen, Z. Spouge, and . Weng, Finding functional sequence elements by multiple local alignment, Nucleic Acids Res, vol.32, issue.1, pp.189-200, 2004.

J. A. Gally and G. M. Edelman, The genetic control of immunoglobulin synthesis, Annual Review of Genetics, vol.6, issue.1, pp.1-46, 1972.
DOI : 10.1146/annurev.ge.06.120172.000245

J. Gao and R. Impagliazzo, Orthogonal vectors is hard for first-order properties on sparse graphs, Electronic Colloquium on Computational Complexity (ECCC), vol.23, p.53, 2016.

R. Grossi, S. Costas, C. Iliopoulos, N. Liu, . Pisanti et al., On-line pattern matching on a set of similar texts, CPM, LIPIcs. Schloss Dagstuhl-Leibniz-Zentrum fuer Informatik, 2017.

D. Gusfield, Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology, 1997.

S. Costas, R. Iliopoulos, S. P. Kundu, and . Pissis, Efficient pattern matching in elasticdegenerate texts, LATA, volume 10168 of LNCS, pp.131-142, 2017.

S. Costas, J. Iliopoulos, and . Radoszewski, Truly Subquadratic-Time Extension Queries and Periodicity Detection in Strings with Uncertainties, CPM, volume 54 of LIPIcs, vol.8, 2016.

R. Impagliazzo and R. Paturi, On the complexity of k-sat, J. Comput. Syst. Sci, vol.62, issue.2, pp.367-375, 2001.

R. Impagliazzo, R. Paturi, and F. Zane, Which problems have strongly exponential complexity?, J. Comput. Syst. Sci, vol.63, issue.4, pp.512-530, 2001.

I. , Commission on Biochemical Nomenclature. Abbreviations and symbols for nucleic acids, polynucleotides, and their constituents, Biochemistry, vol.9, issue.20, pp.4022-4027, 1970.

R. J. Lipton, On The Intersection of Finite Automata, pp.145-148, 2010.

G. Manacher, A new linear-time "on-line" algorithm for finding the smallest initial palindrome of a string, Journal of the ACM, vol.22, issue.3, pp.346-351, 1975.

W. Lee-ann-mccue, S. Thompson, M. P. Carmack, J. S. Ryan, V. Liu et al., Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes, Nucleic Acids Res, vol.29, issue.3, pp.774-782, 2001.

M. Brejnev-muhizi-muhire, B. Golden, P. Murrell, J. Lefeuvre, A. Lett et al., Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic single-stranded DNA viruses, Journal of virology, vol.88, issue.4, pp.1972-1989, 2014.

. Eugene-w-myers, Approximate matching of network expressions with spacers, Journal of Computational Biology, vol.3, issue.1, pp.33-51, 1996.

N. Pisanti, H. Soldano, M. Carpentier, and J. Pothier, A relational extension of the notion of motifs: Application to the common 3d protein substructures searching problem, Journal of Computational Biology, vol.16, issue.12, pp.1635-1660, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00618073