Fast detection of specific fragments against a set of sequences
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We design alignment-free techniques for comparing a sequence or word, called a target, against a set of words, called a reference. A target-specific factor of a target T against a reference R is a factor w of a word in T which is not a factor of a word of R and such that any proper factor of w is a factor of a word of R. We first address the computation of the set of target-specific factors of a target T against a reference R, where T and R are finite sets of sequences. The result is the construction of an automaton accepting the set of all considered target-specific factors. The construction algorithm runs in linear time according to the size of T∪ R. The second result consists in the design of an algorithm to compute all the occurrences in a single sequence T of its target-specific factors against a reference R. The algorithm runs in real-time on the target sequence, independently of the number of occurrences of target-specific factors.
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