# 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

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topMignosi, 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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