fn() alignmentFreeComparison
Computes the pairwise similarity scores for a set of sequences.

Defined in <seqan/alignment_free.h>
Signature void alignmentFreeComparison(scoreMatrix, sequenceSet, score);

Parameters

scoreMatrix A two-dimensional Matrix, used to store all pairwise scores.
sequenceSet StringSet containing all sequences for which pairwise scores will be computed.
score The AFScore object to be used for computing the alignment.

Detailed Description

Examples

Calculate the alignment free sequence similarity of two masked DNA sequences.

using namespace seqan;
StringSet<Dna5String> sequences;
Dna5String seq1 =
    "TAGGTTTTCCGAAAAGGTAGCAACTTTACGTGATCAAACCTCTGACGGGGTTTTCCCCGTCGAAATTGGGTG"
    "TTTCTTGTCTTGTTCTCACTTGGGGCATCTCCGTCAAGCCAAGAAAGTGCTCCCTGGATTCTGTTGCTAACG"
    "AGTCTCCTCTGCATTCCTGCTTGACTGATTGGGCGGACGGGGTGTCCACCTGACGCTGAGTATCGCCGTCAC"
    "GGTGCCACATGTCTTATCTATTCAGGGATCAGAATTTATTCAGGAAATCAGGAGATGCTACACTTGGGTTAT"
    "CGAAGCTCCTTCCAAGGCGTAGCAAGGGCGACTGAGCGCGTAAGCTCTAGATCTCCTCGTGTTGCAACTACA"
    "CGCGCGGGTCACTCGAAACACATAGTATGAACTTAACGACTGCTCGTACTGAACAATGCTGAGGCAGAAGAT"
    "CGCAGACCAGGCATCCCACTGCTTGAAAAAACTATNNNNCTACCCGCCTTTTTATTATCTCATCAGATCAAG";
Dna5String seq2 =
    "ACCGACGATTAGCTTTGTCCGAGTTACAACGGTTCAATAATACAAAGGATGGCATAAACCCATTTGTGTGAA"
    "AGTGCCCATCACATTATGATTCTGTCTACTATGGTTAATTCCCAATATACTCTCGAAAAGAGGGTATGCTCC"
    "CACGGCCATTTACGTCACTAAAAGATAAGATTGCTCAAANNNNNNNNNACTGCCAACTTGCTGGTAGCTTCA"
    "GGGGTTGTCCACAGCGGGGGGTCGTATGCCTTTGTGGTATACCTTACTAGCCGCGCCATGGTGCCTAAGAAT"
    "GAAGTAAAACAATTGATGTGAGACTCGACAGCCAGGCTTCGCGCTAAGGACGCAAAGAAATTCCCTACATCA"
    "GACGGCCGCGNNNAACGATGCTATCGGTTAGGACATTGTGCCCTAGTATGTACATGCCTAATACAATTGGAT"
    "CAAACGTTATTCCCACACACGGGTAGAAGAACNNNNATTACCCGTAGGCACTCCCCGATTCAAGTAGCCGCG";

clear(sequences);
appendValue(sequences, seq1);
appendValue(sequences, seq2);

Matrix<double, 2> myMatrix;

unsigned kmerSize = 5;
unsigned bgModelOrder = 1;
String<char>  revCom = "both_strands";
unsigned mismatches = 1;
double mismatchWeight = 0.5;
AFScore<N2> myScoreN2(kmerSize, bgModelOrder, revCom, mismatches, mismatchWeight);

alignmentFreeComparison(myMatrix, sequences, myScoreN2);
std::cout << myMatrix;

Data Races

Thread safety unknown!