Example Program
Motif Finder
Examples for how to start a motif search using SeqAn's Motif Finder.
File "find_motif.cpp"
1#define SEQAN_DEBUG
2#define SEQAN_TEST
3
4#include "seqan/find_motif.h"
5
6using namespace seqan;
7
8int main() 
9{
10    SEQAN_TREPORT("TEST BEGIN")
11
12    srand((unsigned) time(NULL));
13
Motif search on a small set of nucleotide sequences.
14    unsigned int t = 3;        //number of input sequences
15    unsigned int n = 6;        //length of sequence
16    unsigned int l = 4;        //length of motif
17    unsigned int d = 1;        //number of substitutions
18    bool is_exact = true;    //size of Hamming distance
19    unsigned int h = 0;        //size of the neighborhood considering at first
20
21    String<DnaString> dataset;
22    appendValue(dataset,DnaString("ACAGCA"));
23    appendValue(dataset,DnaString("AGGCAG"));
24    appendValue(dataset,DnaString("TCAGTC"));
25    
Application of ePatternBranching (h=0)
26    MotifFinder<Dna, EPatternBranching> finder_epb1(t,l,d,is_exact,h);
27    findMotif(finder_epb1,dataset,OMOPS());
28    displayResult(finder_epb1); 
29
Application of ePatternBranching (h=0)
30    MotifFinder<Dna, EPatternBranching> finder_epb2(t,l,d,is_exact,h);
31    findMotif(finder_epb2,dataset,OOPS());
32    displayResult(finder_epb2); 
33
Application of PMS1-ZOOPS
34    MotifFinder<Dna, PMS1> finder_pms1(l,d,is_exact);
35    findMotif(finder_pms1,dataset,ZOOPS());
36    displayResult(finder_pms1); 
37
Application of PMSP-TCM
38    MotifFinder<Dna, PMSP> finder_pmsp(l,d,is_exact);
39    findMotif(finder_pmsp,dataset,TCM());
40    displayResult(finder_pmsp); 
41    
Application of PROJECTION-OOPS
42    unsigned int m = t*(n-l+1);
43    MotifFinder<Dna, Projection> finder_proj(t,l,m,d,is_exact);
44    findMotif(finder_proj, dataset, OOPS());
45    displayResult(finder_proj);
46
Application of PROJECTION-OMOPS
47    MotifFinder<Dna, Projection> finder_proj_omops(t,l,m,d,is_exact);
48    findMotif(finder_proj_omops, dataset, OMOPS());
49    displayResult(finder_proj_omops);
50
Application of PROJECTION-ZOOPS
51    MotifFinder<Dna, Projection> finder_proj_zoops(t,l,m,d,is_exact);
52    findMotif(finder_proj_zoops, dataset, ZOOPS());
53    displayResult(finder_proj_zoops);
54    
Application of PROJECTION-TCM
55    MotifFinder<Dna, Projection> finder_proj_tcm(t,l,m,d,is_exact);
56    findMotif(finder_proj_tcm, dataset, TCM());
57    displayResult(finder_proj_tcm);
58
59    SEQAN_TREPORT("TEST END")
60    return 0;
61}
62
Output
projects/tests/find_motif/test_find_motif.cpp(10): TEST BEGIN
[0]: AGCC

[0]: AGCC

[0]: AAGC 
[1]: ACAG
[2]: AGAC
[3]: AGCC
[4]: AGGA
[5]: AGTA
[6]: CAGA
[7]: CAGG
[8]: CCAG
[9]: CGCA
[10]: CGGC
[11]: GCAG
[12]: TCAG
[13]: TGCA

[0]: AAGC
[1]: AAGT
[2]: AATC
[3]: ACAG
[4]: ACGC
[5]: ACTC
[6]: AGAC
[7]: AGCA
[8]: AGCC
[9]: AGGA
[10]: AGGC
[11]: AGGG
[12]: AGGT
[13]: AGTA
[14]: AGTC
[15]: AGTG
[16]: AGTT
[17]: ATGC
[18]: ATTC
[19]: CAAT
[20]: CACT
[21]: CAGA
[22]: CAGC
[23]: CAGG
[24]: CATT
[25]: CCAG
[26]: CCGT
[27]: CGCA
[28]: CGGC
[29]: CGGT
[30]: CGTC
[31]: CTGT
[32]: GAAG
[33]: GACA
[34]: GAGT
[35]: GCAA
[36]: GCAC
[37]: GCAG
[38]: GCAT
[39]: GCCA
[40]: GCCG
[41]: GCGG
[42]: GCTG
[43]: GGAA
[44]: GGAG
[45]: GGCC
[46]: GGCG
[47]: GGCT
[48]: GGGA
[49]: GGGC
[50]: GGTA
[51]: GGTC
[52]: GTAG
[53]: GTCA
[54]: TAAG
[55]: TAGT
[56]: TCAA
[57]: TCAC
[58]: TCAG
[59]: TCAT
[60]: TCCG
[61]: TCGG
[62]: TCTG
[63]: TGAG
[64]: TGCA
[65]: TGGC
[66]: TGTC
[67]: TTAG

AGCC

AGCC

TCAG

TCAG
projects/tests/find_motif/test_find_motif.cpp(82): TEST END
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