fn() calculateOverlapIndicatorCalculate word overlaps: epsilon(word1, word2) = 1 where word2[j] = word1[j+p] for
all j = 1..(k-p).
Calculate word overlaps: epsilon(word1, word2) = 1 where word2[j] = word1[j+p] for
all j = 1..(k-p).
Defined in | <seqan/alignment_free.h> |
---|---|
Signature |
void calculateOverlapIndicator(epsilon, word1, word2);
|
Parameters
epsilon
|
String of int giving the periodicity (overlap indicator) of word1 and word2. |
---|---|
word1
|
String (for example a DNA sequence). |
word2
|
String (for example a DNA sequence). |
Detailed Description
Calculate the indicator for overlaps of two words. The formula is based on (Robin et al., 2005)
References
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.
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
Data Races
Thread safety unknown!