| Function calculateOverlapIndicator Calculate word overlaps: epsilon(word1,word2)= 1 where word2[j]=word1[j+p] for all j=1...(k-p) calculateOverlapIndicator(epsilon, word1, word2) Include Headers seqan/alignment_free.h Parameters
epsilon | String<int> giving the periodicity ("overlap indicator") of word1 and word2 Types: String
word1 | String (for example a DNA sequence) Types: String
word2 | String (for example a DNA sequence) Types: String
Remarks Calculate the indicator for overlaps of two words. The formula is based on Robin, S., Rodolphe, F., and Schbath, S. (2005). DNA, Words and Models. Cambridge University Press. See Jonathan Goeke et al (to appear) for details on the implementation. Return Values String<int> epsilon, the word overlap indicator. Examples Calculate the overlap indicator (epsilon) for two words using namespace seqan; DnaString word1 = "ATATA"; DnaString word2 = "TATAT"; String<int> epsilon; calculateOverlapIndicator(epsilon, word1, word2); for(unsigned i = 0; i < length(epsilon); ++i) std::cout << epsilon[i] << "\t"; // epsilon = 01010: // word1 ATATA // word2 overlap 1: -TATAT // word2 overlap 2: ---TATAT See Also calculateCovariance, alignmentFreeComparison, calculateVariance, calculatePeriodicity SeqAn - Sequence Analysis Library - www.seqan.de

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