| Function alignmentFreeComparison 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; See Also AFScore, stringToStringSet, calculateProbability, calculateCovariance, calculateVariance, calculateOverlapIndicator, countKmers, cutNs, calculatePeriodicity SeqAn - Sequence Analysis Library - www.seqan.de

Page built @2014/10/13 16:12:57