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Palindromic Subsequence Automata and Longest Common Palindromic Subsequence

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Abstract

In this paper, we present a novel weighted finite automaton called palindromic subsequence automaton (PSA) that is a compact representation of all the palindromic subsequences of a string. Then we use PSA to solve the longest common palindromic subsequence problem. Our automata based algorithms are efficient both in theory and in practice.

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References

  1. Breslauer, D., Galil, Z.: Finding all periods and initial palindromes of a string in parallel. Algorithmica 14(4), 355–366 (1995)

    Article  MathSciNet  MATH  Google Scholar 

  2. Chen, K.-Y., Hsu, P.-H., Chao, K.-M.: Identifying approximate palindromes in run-length encoded strings. ISAAC 2, 339–350 (2010)

    MathSciNet  MATH  Google Scholar 

  3. Choi, C.Q.: DNA palindromes found in cancer. The Scientist (2005)

  4. Chowdhury, S.R., Hasan, M.M., Iqbal, S., Rahman, M.S.: Computing a longest common palindromic subsequence. Fundam. Inform. 129(4), 329–340 (2014)

    MathSciNet  MATH  Google Scholar 

  5. Chuang, K., Lee, R., Huang, C.: Finding all palindrome subsequences in a string. In: The 24th Workshop on Combinatorial Mathematics and Computation Theory (2007)

  6. Farhana, E., Rahman, M.S.: Doubly-constrained LCS and hybrid-constrained LCS problems revisited. Inf. Process. Lett. 112(13), 562–565 (2012)

    Article  MathSciNet  MATH  Google Scholar 

  7. Galil, Z.: Real-time algorithms for string-matching and palindrome recognition. In: STOC, pp. 161–173 (1976)

  8. Gusfield, D.: Algorithms on Strings, Trees, and Sequences—Computer Science and Computational Biology. Cambridge University Press, Cambridge (1997)

    Book  MATH  Google Scholar 

  9. Hoshino, H., Shinohara, A., Takeda, M., Arikawa, S.: Online construction of subsequence automata for multiple texts. In: SPIRE, pp. 146–152 (2000)

  10. Hsu, P.-H., Chen, K.-Y., Chao, K.-M.: Finding all approximate gapped palindromes. In: ISAAC, pp. 1084–1093 (2009)

  11. http://0-www.ncbi.nlm.nih.gov.ilsprod.lib.neu.edu/nuccore/acin02000001.1. Accessed 5 Jan 2014

  12. http://www.ncbi.nlm.nih.gov/genomes/genomesgroup.cgi. Accessed 10 July 2014

  13. Hunt, J.W., Szymanski, T.G.: A fast algorithm for computing longest subsequences. Commun. ACM 20(5), 350–353 (1977)

    Article  MathSciNet  MATH  Google Scholar 

  14. Tomohiro, I., Inenaga, S., Takeda, M.: Palindrome pattern matching. In: CPM, pp. 232–245 (2011)

  15. Iliopoulos, C.S., Rahman, M.S.: Algorithms for computing variants of the longest common subsequence problem. Theor. Comput. Sci. 395(2–3), 255–267 (2008)

    Article  MathSciNet  MATH  Google Scholar 

  16. Iliopoulos, C.S., Rahman, M.S.: New efficient algorithms for the LCS and constrained LCS problems. Inf. Process. Lett. 106(1), 13–18 (2008)

    Article  MathSciNet  MATH  Google Scholar 

  17. Iliopoulos, C.S., Rahman, M.S.: A new efficient algorithm for computing the longest common subsequence. Theory Comput. Syst. 45(2), 355–371 (2009)

    Article  MathSciNet  MATH  Google Scholar 

  18. Iliopoulos, C.S., Rahman, M.S., Vorácek, M., Vagner, L.: Finite automata based algorithms on subsequences and supersequences of degenerate strings. J. Discrete Algorithms 8(2), 117–130 (2010)

    Article  MathSciNet  MATH  Google Scholar 

  19. Kolpakov, R., Kucherov, G.: Searching for gapped palindromes. Theor. Comput. Sci. 410(51), 5365–5373 (2009)

    Article  MathSciNet  MATH  Google Scholar 

  20. Manacher, G.K.: A new linear-time on-line algorithm for finding the smallest initial palindrome of a string. J. ACM 22(3), 346–351 (1975)

    Article  MATH  Google Scholar 

  21. Matsubara, W., Inenaga, S., Ishino, A., Shinohara, A., Nakamura, T., Hashimoto, K.: Efficient algorithms to compute compressed longest common substrings and compressed palindromes. Theor. Comput. Sci. 410(8–10), 900–913 (2009)

    Article  MathSciNet  MATH  Google Scholar 

  22. Melichar, B., Holub, J., Muzatko, P.: Language and Translation. Publishing House of CTU (1997)

  23. Porto, A.H.L., Barbosa, V.C.: Finding approximate palindromes in strings. Pattern Recognit. 35(11), 2581–2591 (2002)

    Article  MATH  Google Scholar 

  24. Tanaka, H., Bergstrom, D.A., Yao, M.-C., Tapscott, S.J.: Widespread and nonrandom distribution of dna palindromes in cancer cells provides a structural platform for subsequent gene amplification. Nat. Genet. 37(3), 320–327 (2005)

    Article  Google Scholar 

  25. Tanaka, H., Tapscott, S.J., Trask, B.J., Yao, M.C.: Short inverted repeats initiate gene amplification through the formation of a large DNA palindrome in mammalian cells. Natl. Acad. Sci. 99(13), 8772–8777 (2002)

    Article  Google Scholar 

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Correspondence to M. Sohel Rahman.

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Part of this research work was conducted when M. Sohel Rahman was on a Sabbatical Leave from BUET and was partially supported by a Commonwealth Fellowship.

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Hasan, M.M., Islam, A.S.M.S., Rahman, M.S. et al. Palindromic Subsequence Automata and Longest Common Palindromic Subsequence. Math.Comput.Sci. 11, 219–232 (2017). https://doi.org/10.1007/s11786-016-0288-7

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  • DOI: https://doi.org/10.1007/s11786-016-0288-7

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