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#include <iostream>
#include <seqan/align.h>
#include <seqan/sequence.h>
using namespace seqan;
int main()
{
// Create an alignment between subject and query.
Peptide subject =
"MGLSDGEWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASE"
"DLKKHGATVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISECIIQVLQSKH"
"PGDFGADAQGAMNKALELFRKDMASNYK";
Peptide query =
"MSLTKTERTIIVSMWAKISTQADTIGTETLERLFLSHPQTKTYFPHFDLHPGSA"
"QLRAHGSKVVAAVGDAVKSIDDIGGALSKLSELHAYILRVDPVNFKLLSHCLLVTLAARF"
"PADFTAEAHAAWDKFLSVTEKYR";
Align<Peptide> align;
resize(rows(align), 2);
setSource(row(align, 0), subject);
setSource(row(align, 1), query);
Blosum62 scoringScheme(-1, -12);
globalAlignment(align, scoringScheme);
// Compute the statistics of the alignment.
AlignmentStats stats;
computeAlignmentStats(stats, align, scoringScheme);
std::cout << align
<< "score: " << stats.alignmentScore << "\n"
<< "gap opens: " << stats.numGapOpens << "\n"
<< "gap extensions: " << stats.numGapExtensions << "\n"
<< "num insertions: " << stats.numInsertions << "\n"
<< "num deletions: " << stats.numDeletions << "\n"
<< "num matches: " << stats.numMatches << "\n"
<< "num mismatches: " << stats.numMismatches << "\n"
<< "num positive scores: " << stats.numPositiveScores << "\n"
<< "num negative scores: " << stats.numNegativeScores << "\n"
<< "percent similarity: " << stats.alignmentSimilarity << "\n"
<< "percent identity: " << stats.alignmentIdentity << "\n\n\n";
// Clip alignment rows and compute score of this view.
setClippedEndPosition(row(align, 0), 100);
setClippedEndPosition(row(align, 1), 100);
setClippedBeginPosition(row(align, 0), 5);
setClippedBeginPosition(row(align, 1), 5);
computeAlignmentStats(stats, align, scoringScheme);
std::cout << "Clipping alignment to (5, 100)\n"
<< align
<< "score: " << stats.alignmentScore << "\n"
<< "gap opens: " << stats.numGapOpens << "\n"
<< "gap extensions: " << stats.numGapExtensions << "\n"
<< "num insertions: " << stats.numInsertions << "\n"
<< "num deletions: " << stats.numDeletions << "\n"
<< "num matches: " << stats.numMatches << "\n"
<< "num mismatches: " << stats.numMismatches << "\n"
<< "num positive scores: " << stats.numPositiveScores << "\n"
<< "num negative scores: " << stats.numNegativeScores << "\n"
<< "percent similarity: " << stats.alignmentSimilarity << "\n"
<< "percent identity: " << stats.alignmentIdentity << "\n";
return 0;
}
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