Example Program
Local Alignments
Computing local alignments between two sequences.
File "alignment_local.cpp"
A tutorial about local alignments.
1#include <iostream>
2#include <seqan/align.h>
3
4using namespace seqan;
5
6int main()
7{
Example 1: This program applies the Smith-Waterman algorithm to compute the best local alignment between two given sequences.
8    Align< String<char> > ali;
9    appendValue(rows(ali), "aphilologicaltheorem");
10    appendValue(rows(ali), "bizarreamphibology");
11    ::std::cout << "Score = " << localAlignment(ali, Score<int>(3,-3,-2, -2), SmithWaterman()) << ::std::endl;
12    ::std::cout << ali;
13    ::std::cout << "Aligns Seq1[" << sourceBeginPosition(row(ali, 0)) << ":" << (sourceEndPosition(row(ali, 0))-1) << "]";
14    ::std::cout << " and Seq2[" << sourceBeginPosition(row(ali, 1)) << ":" <<  (sourceEndPosition(row(ali, 1))-1) << "]" << ::std::endl << ::std::endl;
15
16
Example 2: This program applies the Waterman-Eggert algorithm to compute all non-overlapping local alignments with score better than 2.
17    Align< String<Dna> > ali2;
18    appendValue(rows(ali2), "ataagcgtctcg");
19    appendValue(rows(ali2), "tcatagagttgc");
20
21    LocalAlignmentFinder<> finder(ali2);
22    Score<int> scoring(2, -1, -2, 0);
23    while (localAlignment(ali2, finder, scoring, 2, WatermanEggert())) {
24        ::std::cout << "Score = " << getScore(finder) << ::std::endl;
25        ::std::cout << ali2;
26        ::std::cout << "Aligns Seq1[" << sourceBeginPosition(row(ali2, 0)) << ":" << (sourceEndPosition(row(ali2, 0))-1) << "]";
27        ::std::cout << " and Seq2[" << sourceBeginPosition(row(ali2, 1)) << ":" <<  (sourceEndPosition(row(ali2, 1))-1) << "]" << ::std::endl << ::std::endl;
28    }
29
30    return 0;
31}
SeqAn - Sequence Analysis Library - www.seqan.de