Spec D2zAFScore
D2z computes a z-score of the inner product of kmer count vectors

Extends AFScore
All Extended AFScore
Defined in <seqan/alignment_free.h>
Signature template <> struct AFScore<D2z>;

Member Function Overview

Member Variable Overview

Detailed Description

D2z can be used for alignment-free sequence comparison. The algorithm differs from the original implementation by the way masked sequences are handled


Kantorovitz, M. R.; Robinson, G. E., Sinha, S. A statistical method for alignment-free comparison of regulatory sequences. Bioinformatics, 2007.

Member Functions Detail

AFScore::AFScore(kmerSize, bgModelOrder[, verbose]);



kmerSize Size of kmer, unsigned.
bgModelOrder Order of the background Markov model, unsigned.
verbose This option will report progress to standard output; bool, defaults to false.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

Member Variables Detail

unsigned D2zAFScore::bgModelOrder

Order of the background model

unsigned D2zAFScore::kmerSize

Size of the kmers

bool D2zAFScore::verbose

true to enable verbose debug output.