[1] Abrahamson, K.: Generalized string matching. SIAM J. Comput. 16 (1987), 6, 1039–1051. DOI 10.1137/0216067 | MR 0917040 | Zbl 0646.68079

[2] Aho, A. V., Corasick, M. J.: Efficient string matching: an aid to bibliographic search. Commun. ACM 18 (1975), 6, 333–340. DOI 10.1145/360825.360855 | MR 0371172 | Zbl 0301.68048

[3] Allauzen, C., Crochemore, M., Raffinot, M.: Factor oracle: A new structure for pattern matching. In: SOFSEM'99, Theory and Practice of Informatics (J. Pavelka, G. Tel, and M. Bartošek, eds.), Milovy 1999, Lect. Notes Comput. Sci. 1725 (1999), Springer-Verlag, Berlin, pp. 295–310. MR 1784520 | Zbl 0964.68078

[4] Antoniou, P., Holub, J., Iliopoulos, C. S., Melichar, B., Peterlongo, P.: Finding common motifs with gaps using finite automata. In: Implementation and Application of Automata (O. H. Ibarra and H.-C. Yen, eds.), Lect. Notes Comput. Sci. 4094 (2006), Springer-Verlag, Heidelberg, pp. 69–77. MR 2296448 | Zbl 1160.68683

[5] Baeza-Yates, R. A., Gonnet, G. H.: A new approach to text searching. Commun. ACM 35 (1992), 10, 74–82. DOI 10.1145/135239.135243

[6] Baker, B. S.: Parameterized duplication in strings: algorithms and an application to software maintenance. SIAM J. Comput. 26 (1997), 5, 1343–1362. DOI 10.1137/S0097539793246707 | MR 1471985 | Zbl 0885.68085

[7] Blumer, A., Blumer, J., Ehrenfeucht, A., Haussler, D., Chen, M. T., Seiferas, J.: The smallest automaton recognizing the subwords of a text. Theor. Comput. Sci. 40 (1985), 1, 31–44. DOI 10.1016/0304-3975(85)90157-4 | MR 0828515 | Zbl 0574.68070

[8] Blumer, A., Blumer, J., Ehrenfeucht, A., Haussler, D., McConnel, R.: Complete inverted files for efficient text retrieval and analysis. J. Assoc. Comput. Mach. 34 (1987), 3, 578–595. DOI 10.1145/28869.28873 | MR 0904194

[9] Boyer, R. S., Moore, J. S.: A fast string searching algorithm. Commun. ACM 20 (1977), 10, 762–772. DOI 10.1145/359842.359859 | Zbl 1219.68165

[10] Cambouropoulos, E., Crochemore, M., Iliopoulos, C. S., Mouchard, L., Pinzon, Y. J.: Algorithms for computing approximate repetitions in musical sequences. In: Proc. Tenth Australian Workshop on Combinatorial Algorithms (R. Raman and J. Simpson, eds.), AWOCA'99, School of Computing, Curtin University of Technology, Perth 1999, pp. 129–144. Zbl 1008.68043

[11] Commentz-Walter, B.: A string matching algorithm fast on the average. In: Proc. 6th International Colloquium on Automata, Languages and Programming (H. A. Maurer, ed.), Graz 1979, Lect. Notes Comput. Sci. 71 (1979), Springer-Verlag, Berlin, pp. 118–132. Zbl 0407.68092

[12] Crochemore, M.: Transducers and repetitions. Theor. Comput. Sci. 45 (1986), 1, 63–86. DOI 10.1016/0304-3975(86)90041-1 | MR 0865967 | Zbl 0615.68053

[13] Damerau, F.: A technique for computer detection and correction of spelling errors. Commun. ACM 7 (1964), 3, 171–176. DOI 10.1145/363958.363994

[14] Dömölki, B.: An algorithm for syntactical analysis. Comput. Linguistics 3 (1964), 29–46, 1964.

[15] Fischer, M. J., Paterson, M.: String matching and other products. In: Proc. SIAM-AMS Complexity of Computation (R. M. Karp, ed.), Providence 1974, pp. 113–125. MR 0400782 | Zbl 0301.68027

[16] Fredriksson, K., Mozgovoy, M.: Efficient parameterized string matching. Inf. Process. Lett. 100 (2006), 3, 91–96. DOI 10.1016/j.ipl.2006.06.009 | MR 2254198 | Zbl 1185.68282

[17] Galil, Z.: Open problems in stringology. In: Combinatorial Algorithms on Words (A. Apostolico and Z. Galil, eds.), NATO ASI Series F 12 (1985), Springer-Verlag, Berlin, pp. 1–8. MR 0815328 | Zbl 0607.68054

[18] Hamming, R. W.: Error detecting and error correcting codes. The Bell System Techn. J. 29 (1950), 2, 147–160. MR 0035935

[19] Holub, J.: Bit parallelism-NFA simulation. In: Implementation and Application of Automata (B. W. Watson and D. Wood, eds.), Lect. Notes in Comput. Sci. 2494 (2002), Springer-Verlag, Heidelberg, pp. 149–160. Zbl 1015.68524

[20] Holub, J.: Finite automata in pattern matching. In: Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications (M. Elloumi and A. Y. Zomaya, eds.), John Wiley and Sons, 2011, pp. 51–71.

[21] Holub, J., Kadlec, T.: NFA simulation using deterministic state cache. In: London Algorithmics 2008: Theory and Practice (J. Chan, J. W. Daykin, and M. S. Rahman, eds.), College Publications 2009, pp. 152–166.

[22] Holub, J., Melichar, B.: Implementation of nondeterministic finite automata for approximate pattern matching. In: Proc. 3rd International Workshop on Implementing Automata, Rouen 1998, pp. 74–81.

[23] Holub, J., Melichar, B.: Approximate string matching using factor automata. Theor. Comput. Sci. 249 (2000), 2, 30–311. DOI 10.1016/S0304-3975(00)00064-5 | MR 1798315 | Zbl 0949.68088

[24] Holub, J., Smyth, W. F.: Algorithms on indeterminate strings. In: Proc. 14th Australasian Workshop On Combinatorial Algorithms (M. Miller and K. Park, eds.), Seoul National University, Seoul 2003, pp. 36–45.

[25] Holub, J., Smyth, W. F., Wang, S.: Hybrid pattern-matching algorithms on indeterminate strings. In: London Stringology Day and London Algorithmic Workshop 2006 (J. Daykin, M. Mohamed, and K. Steinhoefel, eds.) King's College London Series Texts in Algorithmics 2007, pp. 115–133.

[26] Holub, J., Smyth, W. F., Wang, S.: Fast pattern-matching on indeterminate strings. J. Discret. Algorithms 6 (2008), 1, 37–50. DOI 10.1016/j.jda.2006.10.003 | MR 2397082 | Zbl 1162.68808

[27] Holub, J., Špiller, P.: Practical experiments with NFA simulation. In: Proc. Eindhoven FASTAR Days 2004 (L. Cleophas and B. W. Watson, eds.), TU Eindhoven 2004, The Finite Automata Approaches in Stringology 15, pp. 73–95.

[28] Hopcroft, J. E., Ullman, J. D.: Introduction to automata, languages and computations. Addison-Wesley, Reading 1979. MR 0645539

[29] Huffman, D. A.: The synthesis of sequential switching circuits. J. Franklin Inst. 257 (1954), 161–190, 275–303. DOI 10.1016/0016-0032(54)90574-8 | MR 0062648 | Zbl 0166.27201

[30] Huffman, D. A.: A method for the construction of minimum-redundancy codes. Proc. Inst. Radio Engrs 40 (1952), 9, 1098–1101. Zbl 0137.13605

[31] Iliopoulos, C. S., Jayasekera, I., Melichar, B., Šupol, J.: Weighted degenerated approximate pattern matching. In: Proc. 1st International Conference on Language and Automata Theory and Applications, Tarragona 2007.

[32] Kleene, S. C.: Representation of events in nerve nets and finite automata. Automata Studies (1956), 3–42. MR 0077478

[33] Knuth, D. E., Morris, J. H., Jr, Pratt, V. R.: Fast pattern matching in strings. SIAM J. Comput. 6 (1977), 2, 323–350. DOI 10.1137/0206024 | MR 0451916 | Zbl 0372.68005

[34] Kurtz, S.: Reducing the space requirements of suffix trees. Softw. Pract. Exp. 29 (1999), 13, 1149–1171. DOI 10.1002/(SICI)1097-024X(199911)29:13<1149::AID-SPE274>3.0.CO;2-O

[35] Lahoda, J., Melichar, B.: Pattern matching in text coded by finite translation automaton. In: Proc. 7th International Multiconference Information Society (M. Heričko et al., eds.), Institut Jožef Stefan, Ljubljana 2004, pp. 212–214.

[36] Lahoda, J., Melichar, B.: General pattern matching on regular collage system. In: Proc. Prague Stringology Conference'05 (J. Holub and M. Šimánek, eds.), Czech Technical University in Prague 2005, pp. 153–162.

[37] Levenshtein, V. I.: Binary codes capable of correcting deletions, insertions and reversals. Sov. Phys. Dokl. 6 (1966), 707–710. MR 0189928

[38] McCulloch, W. S., Pitts, W.: A logical calculus of the ideas immanent in nervous activity. Bull. Math. Biophys. 5 (1943), 115–133. DOI 10.1007/BF02478259 | MR 0010388 | Zbl 0063.03860

[39] Mealy, G. H.: A method for synthetizing sequential circuits. Bell System Techn. J. 34 (1955), 5, 1045–1079. DOI 10.1002/j.1538-7305.1955.tb03788.x | MR 0073450

[40] Melichar, B.: Repetitions in text and finite automata. In: Proc. Eindhoven FASTAR Days 2004 (L. Cleophas and B. W. Watson, eds.), TU Eindhoven 2004, pp. 1–46.

[41] Melichar, B., Holub, J.: 6D classification of pattern matching problems. In: Proceedings of the Prague Stringology Club Workshop'97 (J. Holub, ed.), Czech Technical University in Prague, 1997, pp. 24–32. Collaborative Report DC-97-03.

[42] Melichar, B., Holub, J., Polcar, T.: Text searching algorithms. Vol. I: Forward string matching. Textbook for course Text Searching Algorithms, 2005.

[43] Moore, E. F.: Gedanken experiments on sequential machines. Automata Studies (1965), 129–153. MR 0078059

[44] Morris, J. H., Jr, Pratt, V. R.: A Linear Pattern-Matching Algorithm. Report 40, University of California, Berkeley 1970.

[45] Navarro, G., Raffinot, M.: A bit-parallel approach to suffix automata: Fast extended string matching. In: Proc. 9th Annual Symposium on Combinatorial Pattern Matching (M. Farach-Colton, ed.), Lect. Notes in Comput. Sci. 1448, Piscataway, NJ, 1998. Springer-Verlag, Berlin, pp. 14–33. MR 1672618

[46] Rabin, M. O., Scott, D.: Finite automata and their decision problems. IBM J. Res. Dev. 3 (1959) 114–125. DOI 10.1147/rd.32.0114 | MR 0103795 | Zbl 0158.25404

[47] Sellers, P. H.: The theory and computation of evolutionary distances: Pattern recognition. J. Algorithms 1 (1980), 4, 359–373. DOI 10.1016/0196-6774(80)90016-4 | MR 0604870 | Zbl 0454.68110

[48] Shyamasundar, R. K.: A Simple String Matching Algorithm. Technical Report, Tata Institute of Fundamental Research 1976.

[49] M. Šimůnek, Melichar, B.: Borders and finite automata. In: Implementation and Application of Automata (O. H. Ibarra and H.-C. Yen, eds.), Lecture Notes in Comput. Sci. 4094, Springer-Verlag, Heidelberg 2006, pp. 58–68. MR 2296447 | Zbl 1142.68416

[50] Ukkonen, E.: Finding approximate patterns in strings. J. Algorithms 6 (1985), 1–3, 132–137. DOI 10.1016/0196-6774(85)90023-9 | MR 0780855 | Zbl 0566.68072

[51] Voráček, M., Vagner, L., Rahman, S., Iliopoulos, C. S.: The constrained longest common subsequence problem for degenerate strings. In: Implementation and Application of Automata (J. Holub and J. Žďárek, eds.), Lecture Notes in Comput. Sci. 4783, Springer-Verlag, Heidelberg 2007, pp. 309–311. Zbl 1137.68621

[52] Wu, S., Manber, U.: Fast text searching allowing errors. Commun. ACM 35 (1992), 10, 83–91. DOI 10.1145/135239.135244

[53] Ziv, J., Lempel, A.: Compression of individual sequences via variable length coding. IEEE Trans. Inf. Theory 24 (1978), 530–536. DOI 10.1109/TIT.1978.1055934 | MR 0507465