| Example Program Maximal Unique Matches Example for using the MUMs Iterator. Given a set of sequences, a unique match is a match that occurs exactly once in each sequence. A maximal unique match (MUM) is a unique match that is not part of any longer unique match. The following example demonstrates how to iterate over all MUMs and output them. File "index_mums.cpp" A tutorial about finding MUMs.
1 | #include <iostream>
2 | #include <seqan/index.h>
3 |
4 | using namespace seqan;
5 |
6 | int main ()
7 | {
We begin with a StringSet that stores multiple strings.
8 | StringSet< String<char> > mySet;
9 | resize(mySet, 3);
10 | mySet[0] = "SeqAn is a library for sequence analysis.";
11 | mySet[1] = "The String class is the fundamental sequence type in SeqAn.";
12 | mySet[2] = "Subsequences can be handled with SeqAn's Segment class.";
13 |
Then we create an Index of this StringSet.
14 | typedef Index< StringSet<String<char> > > TMyIndex;
15 | TMyIndex myIndex(mySet);
16 |
To find maximal unique matches (MUMs), we use the MUMs Iterator and set the minimum MUM length to 3.
17 | Iterator< TMyIndex, MUMs >::Type myMUMiterator(myIndex, 3);
18 | String< SAValue<TMyIndex>::Type > occs;
19 |
20 | while (!atEnd(myMUMiterator)) {
A multiple match can be represented by the positions it occurs at in every sequence and its length. getOccurrences returns an unordered sequence of pairs (seqNo,seqOfs) the match occurs at.
21 | occs = getOccurrences(myMUMiterator);
To order them ascending according seqNo we use orderOccurrences.
22 | orderOccurrences(occs);
23 |
24 | for(unsigned i = 0; i < length(occs); ++i)
25 | ::std::cout << getValueI2(occs[i]) << ", ";
26 |
repLength returns the length of the match.
27 | ::std::cout << repLength(myMUMiterator) << " ";
28 |
The match string itself can be determined with representative.
29 | ::std::cout << "\t\"" << representative(myMUMiterator) << '\"' << ::std::endl;
30 |
31 | ++myMUMiterator;
32 | }
33 |
34 | return 0;
35 | }
Output The only maximal matches that occur in all 3 sequences are "SeqAn" and "sequence". They occur exactly once and thus are maximal unique matches. weese@tanne:~/seqan$ cd demos weese@tanne:~/seqan/demos$ make index_mums weese@tanne:~/seqan/demos$ ./index_mums 0, 53, 33, 5 "SeqAn" 23, 36, 3, 8 "sequence" weese@tanne:~/seqan/demos$ See getOccurrences, Index, MUMs Iterator, orderOccurrences, repLength, representative, StringSet SeqAn - Sequence Analysis Library - www.seqan.de