A. V. Aho, J. E. Hopcroft, and J. D. Ullman, Data Structures and Algorithms, 1983.

R. Badii and A. Politi, Complexity, Hierarchical Structures and Scaling in Physics, 1997.

M. P. Béal, M. Crochemore, and G. Fici, Presentations of Constrained Systems With Unconstrained Positions, IEEE Transactions on Information Theory, vol.51, issue.5, pp.1891-1900, 2005.
DOI : 10.1109/TIT.2005.846423

M. P. Béal, M. Crochemore, F. Mignosi, A. Restivo, and M. Sciortino, Computing forbidden words of regular languages, Fund. Inform, vol.56, issue.12, pp.121-135, 2003.

M. P. Béal, F. Fiorenzi, and F. Mignosi, MINIMAL FORBIDDEN PATTERNS OF MULTI-DIMENSIONAL SHIFTS, International Journal of Algebra and Computation, vol.15, issue.01, pp.73-93, 2005.
DOI : 10.1142/S0218196705002165

M. P. Béal, F. Mignosi, A. Restivo, and M. Sciortino, Forbidden Words in Symbolic Dynamics, Advances in Applied Mathematics, vol.25, issue.2, pp.163-193, 2000.
DOI : 10.1006/aama.2000.0682

A. Blumer, J. Blumer, A. Ehrenfeucht, D. Haussler, and R. Mcconnell, Linear size finite automata for the set of all subwords of a word : an outline of results, Bull. European Assoc. Theoret. Comput. Sci, vol.21, pp.12-20, 1983.

A. Blumer, J. Blumer, A. Ehrenfeucht, D. Haussler, and R. Mcconnell, Building a complete inverted file for a set of text files in linear time, Proceedings of the sixteenth annual ACM symposium on Theory of computing , STOC '84, pp.349-351, 1984.
DOI : 10.1145/800057.808700

A. Blumer, J. Blumer, D. Haussler, R. Mcconnell, and A. Ehrenfeucht, Complete inverted files for efficient text retrieval and analysis, Journal of the ACM, vol.34, issue.3, pp.578-595, 1987.
DOI : 10.1145/28869.28873

D. Breslauer and R. Hariharan, OPTIMAL PARALLEL CONSTRUCTION OF MINIMAL SUFFIX AND FACTOR AUTOMATA, Parallel Processing Letters, vol.06, issue.01, pp.35-44, 1996.
DOI : 10.1142/S0129626496000054

J. Campello-de-souza, B. H. Marcus, R. New, and B. A. Wilson, Constrained systems with unconstrained positions, IEEE Transactions on Information Theory, vol.48, issue.4, pp.866-879, 2002.
DOI : 10.1109/18.992774

A. Carpi and A. De-luca, Repetitions and Boxes in Words and Pictures, Jewels are Forever, pp.295-306, 1999.
DOI : 10.1007/978-3-642-60207-8_26

A. Carpi and A. De-luca, Special factors, periodicity, and an application to Sturmian words, Acta Informatica, vol.36, issue.12, pp.983-1006, 2000.
DOI : 10.1007/PL00013299

A. Carpi and A. De-luca, Periodic-like words, periodicity, and boxes, Acta Informatica, vol.37, issue.8, pp.597-618, 2001.
DOI : 10.1007/PL00013314

A. Carpi and A. De-luca, Some generalizations of periodic words, Bull. Belg. Math. Soc, vol.8, pp.257-275, 2001.

A. Carpi and A. De-luca, Words and repeated factors, Séminaire Lotharingien de Combinatoire B421, The Andrews Festschrift, pp.231-251, 1999.
DOI : 10.1007/978-3-642-56513-7_12
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.93.4082

A. Carpi and A. De-luca, Words and special factors, Theoretical Computer Science, vol.259, issue.1-2, pp.145-182, 2001.
DOI : 10.1016/S0304-3975(99)00334-5

A. Carpi and A. De-luca, A combinatorial property of the factor poset of a word, Information Processing Letters, vol.81, issue.1, pp.35-39, 2002.
DOI : 10.1016/S0020-0190(01)00192-2

A. Carpi and A. De-luca, On the distribution of characteristic parameters of words, RAIRO - Theoretical Informatics and Applications, vol.36, issue.1, pp.67-96, 2002.
DOI : 10.1051/ita:2002006

A. Carpi and A. De-luca, On the distribution of characteristic parameters of words II, RAIRO - Theoretical Informatics and Applications, vol.36, issue.1, pp.97-127, 2002.
DOI : 10.1051/ita:2002005

A. Carpi and A. De-luca, Semiperiodic words and root-conjugacy, Theoretical Computer Science, vol.292, issue.1, pp.111-130, 2003.
DOI : 10.1016/S0304-3975(01)00218-3
URL : http://doi.org/10.1016/s0304-3975(01)00218-3

A. Carpi, A. De-luca, and S. Varricchio, Special Factors and Uniqueness Conditions in Rational Trees, Theory of Computing Systems, vol.34, issue.4, pp.375-395, 2001.
DOI : 10.1007/s00224-001-1006-6

A. Carpi, A. De-luca, and S. Varricchio, Words, univalent factors, and boxes, Acta Informatica, vol.38, issue.6, pp.409-436, 2002.
DOI : 10.1007/s002360100079
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.108.7748

M. Crochemore and C. Hancart, Pattern matching automata, Handbook of Formal Languages, volume 2 Linear Modeling: Background and Application, chapter 9, pp.399-462, 1997.
DOI : 10.1017/CBO9780511546853.003

M. Crochemore, F. Mignosi, and A. Restivo, Automata and forbidden words, Information Processing Letters, vol.67, issue.3, pp.111-117, 1998.
DOI : 10.1016/S0020-0190(98)00104-5
URL : https://hal.archives-ouvertes.fr/hal-00619578

M. Crochemore, F. Mignosi, and A. Restivo, Minimal forbidden words and factor automata, In Mathematical Foundations of Computer Science Lect. Notes Comput. Sci, vol.1450, pp.665-673, 1998.
DOI : 10.1007/BFb0055817
URL : https://hal.archives-ouvertes.fr/hal-00619990

M. Crochemore, F. Mignosi, A. Restivo, and S. Salemi, Data compression using antidictionaries, Proceedings of the IEEE Lossless Data Compression, pp.1756-1768, 2000.
DOI : 10.1109/5.892711
URL : https://hal.archives-ouvertes.fr/hal-00619579

S. Eilenberg, Automata, Languages and Machines, volume A, 1974.

G. Fici, F. Mignosi, M. Sciortino, and A. Restivo, Word assembly through minimal forbidden words, Theoretical Computer Science, vol.359, issue.1-3
DOI : 10.1016/j.tcs.2006.03.006
URL : https://hal.archives-ouvertes.fr/hal-00619719

G. Fici, F. Mignosi, M. Sciortino, and A. Restivo, Fragment assembly through minimal forbidden words, 2004.

A. Gabriele, F. Mignosi, A. Restivo, and M. Sciortino, Indexing Structures for Approximate String Matching, Algorithms and Complexity: 5th Italian Conference, CIAC 2003 Proceedings, volume 2653, pp.140-151, 2003.
DOI : 10.1007/3-540-44849-7_20

D. Gusfield, Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology, 1997.
DOI : 10.1017/CBO9780511574931

D. A. Lind and B. H. Marcus, An Introduction to Symbolic Dynamics and Coding, 1995.
DOI : 10.1017/CBO9780511626302

M. Lothaire, Combinatorics on Words, 1983.
DOI : 10.1017/CBO9780511566097
URL : https://hal.archives-ouvertes.fr/hal-00620607

M. Lothaire, Algebraic Combinatorics on Words, 2002.
DOI : 10.1017/CBO9781107326019
URL : https://hal.archives-ouvertes.fr/hal-00620608

M. Lothaire, Applied Combinatorics on Words, 2005.
DOI : 10.1017/CBO9781107341005
URL : https://hal.archives-ouvertes.fr/hal-00620607

B. Marcus, P. Chaichanavong, and T. ?. Poo, Trade-off functions for constrained systems with unconstrained positions, IEEE Trans. Inform. Theory

B. H. Marcus, Sofic systems and encoding data, IEEE Transactions on Information Theory, vol.31, issue.3, pp.266-377, 1985.
DOI : 10.1109/TIT.1985.1057037

B. H. Marcus, R. M. Roth, and P. H. Siegel, Constrained systems and coding for recording channels, Handbook of Coding Theory, pp.1635-1764, 1998.

F. Mignosi, A. Restivo, and M. Sciortino, Forbidden Factors in Finite and Infinite Words, Jewels are Forever, pp.339-350, 1999.
DOI : 10.1007/978-3-642-60207-8_30

F. Mignosi, A. Restivo, and M. Sciortino, Forbidden Factors and Fragment Assembly, RAIRO - Theoretical Informatics and Applications, vol.35, issue.6, pp.565-577, 2001.
DOI : 10.1051/ita:2001132

F. Mignosi, A. Restivo, and M. Sciortino, Forbidden Factors and Fragment Assembly, Developments in Language Theory, pp.349-358, 2001.
DOI : 10.1051/ita:2001132

F. Mignosi, A. Restivo, and M. Sciortino, Words and forbidden factors, Theoretical Computer Science, vol.273, issue.1-2, pp.99-117, 1999.
DOI : 10.1016/S0304-3975(00)00436-9

F. Mignosi, A. Restivo, M. Sciortino, and J. Storer, On Sequence Assembly, 2000.

B. E. Moision and P. H. Siegel, Periodic-finite-type shift spaces, Proceedings. 2001 IEEE International Symposium on Information Theory (IEEE Cat. No.01CH37252), 2001.
DOI : 10.1109/ISIT.2001.935928
URL : https://hal.archives-ouvertes.fr/hal-00619782

J. Moon and B. Brickner, Maximum transition run codes for data storage systems, IEEE Transactions on Magnetics, vol.32, issue.5, pp.3992-3994, 1996.
DOI : 10.1109/20.539241

E. W. Myers, Adavances in sequence assembly, Automata DNA Sequencing and Analysis, pp.231-238, 1994.

P. A. Pevzner, H. Tang, and M. S. Waterman, A new approach to fragment assembly in DNA sequencing, Proceedings of the fifth annual international conference on Computational biology , RECOMB '01, pp.256-267, 2001.
DOI : 10.1145/369133.369230

P. A. Pevzner, H. Tang, and M. S. Waterman, An Eulerian path approach to DNA fragment assembly, Proc. Nat. Acad. Sci, pp.9748-9753, 2001.
DOI : 10.1073/pnas.171285098

M. Raffinot, Structures pour la localisation de motifs, 1999.

D. Revuz, Minimisation of acyclic deterministic automata in linear time, Theoretical Computer Science, vol.92, issue.1, pp.181-189, 1992.
DOI : 10.1016/0304-3975(92)90142-3
URL : https://hal.archives-ouvertes.fr/hal-00619678

G. Rozenberg and A. Salomaa, Linear Modeling: Background and Application, Handbook of Formal Languages, 1997.

M. T. Tammi, The principles of shotgun sequencing and automated fragment assembly, Genomics and Bioinformatics Karolinska Institutet, 2003.

M. Weinard and G. Schnitger, On the Greedy Superstring Conjecture, Foundations of Software Technology and Theoretical Computer Science (23rd Conference, pp.387-398, 2003.
DOI : 10.1137/040619144

A. Wijngaarden and K. S. Immink, Maximum runlength-limited codes with error control capabilities, IEEE Journal on Selected Areas in Communications, vol.19, issue.4, pp.602-611, 2001.
DOI : 10.1109/49.920169