Local Alignments

Example Program

Local Alignments

Computing local alignments between two sequences.

A tutorial about local alignments.

1	#include <iostream>
2	#include <seqan/score.h>
3	#include <seqan/align.h>
4
5	using namespace seqan;
6
7	int main()
8	{

Example 1: This program applies the Smith-Waterman algorithm to compute the best local alignment between two given sequences.

9	StringSet<CharString> strings;
10	Align<String<char> > ali;
11	resize(rows(ali), 2);
12	assignSource(row(ali, 0), "aphilologicaltheorem");
13	assignSource(row(ali, 1), "bizarreamphibology");
14	int score = localAlignment(ali, Score<int>(3,-3,-2, -2));
15	std::cout << "Score = " << score << std::endl;
16	std::cout << ali;
17	unsigned cBeginPos = clippedBeginPosition(row(ali, 0));
18	unsigned cEndPos = clippedEndPosition(row(ali, 0)) - 1;
19	std::cout << "Aligns Seq1[" << cBeginPos << ":" << cEndPos << "]";
20	std::cout << " and Seq2[" << cBeginPos << ":" << cEndPos << "]" << std::endl << std::endl;
21
22

Example 2: This program applies the Waterman-Eggert algorithm to compute all non-overlapping local alignments with score better or equal 2.

23	Align<String<Dna> > ali2;
24	resize(rows(ali2), 2);
25	assignSource(row(ali2, 0), "ataagcgtctcg");
26	assignSource(row(ali2, 1), "tcatagagttgc");
27
28	Score<int> scoring(2, -1, -2, 0);
29	LocalAlignmentEnumerator<Score<int>, Unbanded> enumerator(scoring, 2);
30	while (nextLocalAlignment(ali2, enumerator))
31	{
32	std::cout << "Score = " << getScore(enumerator) << std::endl;
33	std::cout << ali2;
34	unsigned cBeginPos0 = clippedBeginPosition(row(ali2, 0));
35	unsigned cEndPos0 = clippedEndPosition(row(ali2, 0)) - 1;
36	unsigned cBeginPos1 = clippedBeginPosition(row(ali2, 1));
37	unsigned cEndPos1 = clippedBeginPosition(row(ali2, 1)) - 1;
38	std::cout << "Aligns Seq1[" << cBeginPos0 << ":" << cEndPos0 << "]";
39	std::cout << " and Seq2[" << cBeginPos1 << ":" << cEndPos1 << "]";
40	std::cout << std::endl << std::endl;
41	}
42

Example 3

43	Align<String<Dna> > ali3;
44	resize(rows(ali3), 2);
45	assignSource(row(ali3, 0), "cccccc");
46	assignSource(row(ali3, 1), "tttttggccccccgg");
47
48	Score<int> scoring3(1, -1, -1, -1);
49	LocalAlignmentEnumerator<Score<int>, Unbanded> enumerator3(scoring3, 5);
50	while (nextLocalAlignment(ali3, enumerator3))
51	{
52	std::cout << "Score = " << getScore(enumerator3) << std::endl;
53	std::cout << ali3;
54	unsigned cBeginPos0 = clippedBeginPosition(row(ali3, 0));
55	unsigned cEndPos0 = clippedEndPosition(row(ali3, 0)) - 1;
56	unsigned cBeginPos1 = clippedBeginPosition(row(ali3, 1));
57	unsigned cEndPos1 = clippedEndPosition(row(ali3, 1)) - 1;
58	std::cout << "Aligns Seq1[" << cBeginPos0 << ":" << cEndPos0 << "]";
59	std::cout << " and Seq2[" << cBeginPos1 << ":" << cEndPos1 << "]";
60	std::cout << std::endl << std::endl;
61	}
62

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.

63	Align<String<Dna5> > ali4;
64	resize(rows(ali4), 2);
65	assignSource(row(ali4, 0), "AAAAAAANAAAGGGNGGGGGGGGNGGGGGANAA");
66	assignSource(row(ali4, 1), "GGGGGGCGGGGGGGA");
67
68	LocalAlignmentFinder<> finder4(ali4);
69	Score<int> scoring4(1, -1, -1, -1);
70	LocalAlignmentEnumerator<Score<int>, Banded> enumerator4(scoring3, -1, 8, 5);
71	while (nextLocalAlignment(ali4, enumerator4))
72	{
73	std::cout << "Score = " << getScore(enumerator4) << std::endl;
74	std::cout << ali4;
75	unsigned cBeginPos0 = clippedBeginPosition(row(ali4, 0));
76	unsigned cEndPos0 = clippedEndPosition(row(ali4, 0)) - 1;
77	unsigned cBeginPos1 = clippedBeginPosition(row(ali4, 1));
78	unsigned cEndPos1 = clippedEndPosition(row(ali4, 1)) - 1;
79	std::cout << "Aligns Seq1[" << cBeginPos0 << ":" << cEndPos0 << "]";
80	std::cout << " and Seq2[" << cBeginPos1 << ":" << cEndPos1 << "]";
81	std::cout << std::endl << std::endl;
82	}
83
84	return 0;
85	}

See

localAlignment, Score, Align

SeqAn - Sequence Analysis Library - www.seqan.de