Forbidden Factors and Fragment Assembly

F. Mignosi; A. Restivo; M. Sciortino

RAIRO - Theoretical Informatics and Applications (2010)

  • Volume: 35, Issue: 6, page 565-577
  • ISSN: 0988-3754

Abstract

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In this paper methods and results related to the notion of minimal forbidden words are applied to the fragment assembly problem. The fragment assembly problem can be formulated, in its simplest form, as follows: reconstruct a word w from a given set I of substrings (fragments) of a word w. We introduce an hypothesis involving the set of fragments I and the maximal length m(w) of the minimal forbidden factors of w. Such hypothesis allows us to reconstruct uniquely the word w from the set I in linear time. We prove also that, if w is a word randomly generated by a memoryless source with identical symbol probabilities, m(w) is logarithmic with respect to the size of w. This result shows that our reconstruction algorithm is suited to approach the above problem in several practical applications e.g. in the case of DNA sequences.

How to cite

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Mignosi, F., Restivo, A., and Sciortino, M.. "Forbidden Factors and Fragment Assembly." RAIRO - Theoretical Informatics and Applications 35.6 (2010): 565-577. <http://eudml.org/doc/222018>.

@article{Mignosi2010,
abstract = { In this paper methods and results related to the notion of minimal forbidden words are applied to the fragment assembly problem. The fragment assembly problem can be formulated, in its simplest form, as follows: reconstruct a word w from a given set I of substrings (fragments) of a word w. We introduce an hypothesis involving the set of fragments I and the maximal length m(w) of the minimal forbidden factors of w. Such hypothesis allows us to reconstruct uniquely the word w from the set I in linear time. We prove also that, if w is a word randomly generated by a memoryless source with identical symbol probabilities, m(w) is logarithmic with respect to the size of w. This result shows that our reconstruction algorithm is suited to approach the above problem in several practical applications e.g. in the case of DNA sequences. },
author = {Mignosi, F., Restivo, A., Sciortino, M.},
journal = {RAIRO - Theoretical Informatics and Applications},
keywords = {Factor automaton; minimal forbidden factor; fragment assembly.; minimal forbidden words},
language = {eng},
month = {3},
number = {6},
pages = {565-577},
publisher = {EDP Sciences},
title = {Forbidden Factors and Fragment Assembly},
url = {http://eudml.org/doc/222018},
volume = {35},
year = {2010},
}

TY - JOUR
AU - Mignosi, F.
AU - Restivo, A.
AU - Sciortino, M.
TI - Forbidden Factors and Fragment Assembly
JO - RAIRO - Theoretical Informatics and Applications
DA - 2010/3//
PB - EDP Sciences
VL - 35
IS - 6
SP - 565
EP - 577
AB - In this paper methods and results related to the notion of minimal forbidden words are applied to the fragment assembly problem. The fragment assembly problem can be formulated, in its simplest form, as follows: reconstruct a word w from a given set I of substrings (fragments) of a word w. We introduce an hypothesis involving the set of fragments I and the maximal length m(w) of the minimal forbidden factors of w. Such hypothesis allows us to reconstruct uniquely the word w from the set I in linear time. We prove also that, if w is a word randomly generated by a memoryless source with identical symbol probabilities, m(w) is logarithmic with respect to the size of w. This result shows that our reconstruction algorithm is suited to approach the above problem in several practical applications e.g. in the case of DNA sequences.
LA - eng
KW - Factor automaton; minimal forbidden factor; fragment assembly.; minimal forbidden words
UR - http://eudml.org/doc/222018
ER -

References

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  1. A.V. Aho, J.E. Hopcroft and J.D. Ullman, Data Structures and Algorithms. Addison Wesley, Reading, Mass (1983).  
  2. M.-P. Béal, F. Mignosi, A. Restivo and M. Sciortino, Forbidden Words in Symbolic Dynamics. Adv. in Appl. Math.25 (2000) 163-193.  
  3. A. Blumer, J. Blumer, A. Ehrenfeucht, D. Haussler, M.T. Chen and J. Seiferas, The smallest automaton recognizing the subwords of a text. Theoret. Comput. Sci.40 (1985) 31-55.  
  4. A. Carpi, A. de Luca and S. Varricchio, Words, univalent factors, and boxes. Acta Inform. (to appear).  
  5. M. Crochemore and C. Hancart, Automata for matching patterns, in Handbook of Formal Languages, Vol. 2, Chap. 9, edited by G. Rosenberg and A. Salomaan. Springer (1997) 399-462.  
  6. M. Crochemore, F. Mignosi and A. Restivo, Automata and forbidden words. Inform. Process. Lett.67 (1998) 111-117.  
  7. M. Crochemore, F. Mignosi, A. Restivo and S. Salemi, Data compression using antidictionaries, in Proc. of the IEEE, Special Issue on Lossless Data Compression, Vol. 88, edited by J.A. Storer (2000) 1756-1768.  
  8. A. Frieze and B.V. Halldórsson, Optimal Sequencing by Hybridization in Rounds, in Proc. of RECOMB 2001, edited by T. Lengauer, D. Sankoff, S. Istrail, P. Pevzner and M. Waterman. ACM Press (2001) 141-148  
  9. D. Gusfield, Algorithms on strings, trees, and sequences: Computer science and computational biology. Cambridge University Press (1997).  
  10. R. Idury and M. Waterman, A new algorithm for DNA sequence assembly. J. Comput. Biol.2 (1995) 291-306.  
  11. F. Mignosi and A. Restivo, Periodicity, in M. Lothaire, Algebraic Combinatorics on Words, Chap. 8. Cambridge University Press (to appear) 237-274. Also available at url: http://www-igm.univ-mlv.fr/ berstel/Lothaire/index.html  
  12. F. Mignosi, A. Restivo and M. Sciortino, Forbidden Factors and Fragment Assembly. Lecture Notes in Comput. Sci. (2001). Proceedings of DLT'01.  
  13. F. Mignosi, A. Restivo and M. Sciortino, Words and Forbidden Factors. Theoret. Comput. Sci.273 (2002) 99-117.  
  14. F. Mignosi, A. Restivo, M. Sciortino and J. Storer, On Sequence Assembly, Technical Report cs-00-210. Brandeis University (2000).  
  15. S. Muthukrishnan and S.C. Sahinalp, Approximate nearest neighbors and sequence comparison with block operations. ACM Press (2000). Proceedings of STOC 2000.  
  16. G. Myers, Whole-Genome DNA Sequencing, IEEE Comput. Engrg. Sci.3 (1999) 33-43.  
  17. H. Peltola, H. Soderlund and E. Ukkonen, SEQAID: A DNA Sequence Assembly Program Based on a Mathematical Model. Nucl. Acids Res.12 (1984) 307-321.  
  18. M. Peltola, H. Soderlund, J. Tarhio and E. Ukkonen, Algorithms for some string matching problems arising in molecular genetics, in Proc. of the 9th IFIP World Computer Congress (1983) 59-64.  
  19. P.A. Pevzner, H. Tang and M. Waterman, A New Approach Fragment Assembly in DNA Sequencing, in Proc. of RECOMB 2001, edited by T. Lengauer, D. Sankoff, S. Istrail, P. Pevzner and M. Waterman. ACM Press (2001) 141-148.  
  20. R. Shamir and D. Tsur, Large Scale Sequencing by Hybridization, in Proc. of RECOMB 2001, edited by T. Lengauer, D. Sankoff, S. Istrail, P. Pevzner and M. Waterman. ACM Press (2001) 269-278.  
  21. M.S. Waterman, Introduction to computational biology: Maps, sequences and genomes. Chapman & Hall (1995).  

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