Local Alignments

Example Program

Local Alignments

Computing local alignments between two sequences.

A tutorial about local alignments.

1	#include <iostream>
2	#include <seqan/align.h>
3
4	using namespace seqan;
5
6	int 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[" << clippedBeginPosition(row(ali, 0)) << ":" << (clippedEndPosition(row(ali, 0))-1) << "]";
14	::std::cout << " and Seq2[" << clippedBeginPosition(row(ali, 1)) << ":" << (clippedEndPosition(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 or equal 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[" << clippedBeginPosition(row(ali2, 0)) << ":" << (clippedEndPosition(row(ali2, 0))-1) << "]";
27	::std::cout << " and Seq2[" << clippedBeginPosition(row(ali2, 1)) << ":" << (clippedEndPosition(row(ali2, 1))-1) << "]" << ::std::endl << ::std::endl;
28	}
29

Example 3

30	Align< String<Dna> > ali3;
31	appendValue(rows(ali3), "cccccc");
32	appendValue(rows(ali3), "tttttggccccccgg");
33	LocalAlignmentFinder<> finder3(ali3);
34	Score<int> scoring3(1, -1, -1, -1);
35	while (localAlignment(ali3, finder3, scoring3, 5, WatermanEggert())) {
36	::std::cout << "Score = " << getScore(finder3) << ::std::endl;
37	::std::cout << ali3;
38	::std::cout << "Aligns Seq1[" << clippedBeginPosition(row(ali3, 0)) << ":" << (clippedEndPosition(row(ali3, 0))-1) << "]";
39	::std::cout << " and Seq2[" << clippedBeginPosition(row(ali3, 1)) << ":" << (clippedEndPosition(row(ali3, 1))-1) << "]" << ::std::endl << ::std::endl;
40	}
41

Example 4: This program applies the banded Waterman-Eggert algorithm to compute all non-overlapping local alignments with score or equal 5 in the band from diagonal -1 to diagonal 8.

42	Align< String<Dna5> > ali4;
43	appendValue(rows(ali4), "AAAAAAANAAAGGGNGGGGGGGGNGGGGGANAA");
44	appendValue(rows(ali4), "GGGGGGCGGGGGGGA");
45
46	LocalAlignmentFinder<> finder4(ali4);
47	Score<int> scoring4(1, -1, -1, -1);
48	while (localAlignment(ali4, finder4, scoring4, 5, -1, 8, BandedWatermanEggert())) {
49	::std::cout << "Score = " << getScore(finder4) << ::std::endl;
50	::std::cout << ali4;
51	::std::cout << "Aligns Seq1[" << clippedBeginPosition(row(ali4, 0)) << ":" << (clippedEndPosition(row(ali4, 0))-1) << "]";
52	::std::cout << " and Seq2[" << clippedBeginPosition(row(ali4, 1)) << ":" << (clippedEndPosition(row(ali4, 1))-1) << "]" << ::std::endl << ::std::endl;
53	}
54
55	return 0;
56	}

See

localAlignment, Score, Align

SeqAn - Sequence Analysis Library - www.seqan.de