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