Spec N2 AFScore
N2 computes the inner product of the standardised neighbourhood kmer count vectors.

Extends AFScore
All Extended AFScore
Defined in <seqan/alignment_free.h>
Signature template <> struct AFScore<N2>;

Member Function Overview

Member Variable Overview

Detailed Description

N2 can be used for alignment-free sequence comparison.


Jonathan Goeke, Marcel H. Schulz, Julia Lasserre, and Martin Vingron. timation of Pairwise Sequence Similarity of Mammalian Enhancers with Word Neighbourhood Counts. Bioinformatics 012).

Member Functions Detail

AFScore::AFScore(kmerSize, bgModelOrder, outputFile, verbose); AFScore::AFScore(kmerSize, bgModelOrder, revCom, outputFile, verbose); AFScore::AFScore(kmerSize, bgModelOrder, revCom, mismatches, mismatchWeight, outputFile, verbose);



kmerSize Size of kmer, unsigned.
bgModelOrder Order of the background Markov model, unsigned.
outputFile When specified, all normalised and standardised kmer neighbourhood counts will be written to this file for every sequence, CharString.
revCom Scoring of reverse complements words [''/'max'/'min'/'mean'/'both_strands'/], CharString.
verbose This option will report progress to standard output, bool, defaults to false.
mismatches Includes words with one mismatch into the word neighbourhood, unsigned, 0 or 1.
mismatchWeight Weight of word counts with one mismatch, double.

See Also

Member Variables Detail

unsigned N2AFScore::bgModelOrder

Order of the background model

unsigned N2AFScore::kmerSize

Size of the kmers.

unsigned N2AFScore::mismatches

Approximate word matches [0(exact)/1(one mismatch)]

double N2AFScore::mismatchWeight

Weight for approximate word matches

CharString N2AFScore::outputFile

When specified, all kmerWeights for every sequence will be written to this file.

CharString N2AFScore::revCom

Scoring of reverse complements words, CharString [''/'max'/'min'/'mean'/'both_strands'/].

bool N2AFScore::verbose

true to enable verbose debug output.