fn() alignmentFreeComparisonComputes the pairwise similarity scores for a set of sequences.
Computes the pairwise similarity scores for a set of sequences.
Defined in | <seqan/alignment_free.h> |
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Signature |
void alignmentFreeComparison(scoreMatrix, sequenceSet, score);
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Parameters
scoreMatrix
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A two-dimensional Matrix, used to store all pairwise scores. |
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sequenceSet
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StringSet containing all sequences for which pairwise scores will be computed. |
score
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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
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