| Function calculatePeriodicity Calculate word periodicity (indicator for overlaps) calculatePeriodicity(periodicity, word1, word2) Include Headers seqan/alignment_free.h Parameters
periodicity | 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 word periodicity (indicator for overlaps) for two words. Return Values String<int> periodicity, the word overlap indicator. Examples Calculate the periodicity of two words (At which positions can they overlap?) using namespace seqan; DnaString word1 = "ATATA"; DnaString word2 = "TATAT"; String<int> periodicity; calculatePeriodicity(periodicity, word1, word2); for(unsigned i = 0; i < length(periodicity); ++i) // Print the periodicity std::cout << periodicity[i] << "\t"; // periodocity[0] = 1: // i = 01234 // word1 = ATATA // word2 = -TATAT // periodocity[1] = 3: // i = 01234 // word1 = ATATA // word2 = ---TATAT See Also calculateCovariance, alignmentFreeComparison, calculateVariance, calculateOverlapIndicator SeqAn - Sequence Analysis Library - www.seqan.de

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