calculateOverlapIndicator

Function

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