alignmentFreeComparison

Function

Computes the pairwise similarity scores for a set of sequences

alignmentFreeComparison(scoreMatrix, sequenceSet, score)

Include Headers

seqan/alignment_free.h

Parameters

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

Examples

Calculate the alignment free sequence similarity o 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;