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> |
---|---|
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!