Abstract
We consider the problem of finding pairs of short patterns such that, in a given input sequence of length n, the distance between each pair's patterns is at least α. The problem was introduced in [1] and is motivated by the optimization of multiplexed nested PCR. We study algorithms for the following two cases; the special case when the two patterns in the pair are required to have the same length, and the more general case when the patterns can have different lengths. For the first case we present an O(αn log log n) time and O(n) space algorithm, and for the general case we give an O(αn log n) time and O(n) space algorithm. The algorithms work for any alphabet size and use asymptotically less space than the algorithms presented in [1]. For alphabets of constant size we also give an O(n√n log2 n) time algorithm for the general case. We demonstrate that the algorithms perform well in practice and present our findings for the human genome. In addition, we study an extended version of the problem where patterns in the pair occur at certain positions at a distance at most α, but do not occur α-close anywhere else, in the input sequence.
| Original language | English |
|---|---|
| Title of host publication | String Processing and Information Retrieval - 12th International Conference, SPIRE 2005, Proceedings |
| Pages | 167-178 |
| Number of pages | 12 |
| DOIs | |
| Publication status | Published - Dec 1 2005 |
| Event | 12th International Conference on String Processing and Information Retrieval, SPIRE 2005 - Buenos Aires, Argentina Duration: Nov 2 2005 → Nov 4 2005 |
Publication series
| Name | Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) |
|---|---|
| Volume | 3772 LNCS |
| ISSN (Print) | 0302-9743 |
| ISSN (Electronic) | 1611-3349 |
Other
| Other | 12th International Conference on String Processing and Information Retrieval, SPIRE 2005 |
|---|---|
| Country | Argentina |
| City | Buenos Aires |
| Period | 11/2/05 → 11/4/05 |
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All Science Journal Classification (ASJC) codes
- Theoretical Computer Science
- Computer Science(all)
Cite this
Composite pattern discovery for PCR application. / Angelov, Stanislav; Inenaga, Shunsuke.
String Processing and Information Retrieval - 12th International Conference, SPIRE 2005, Proceedings. 2005. p. 167-178 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 3772 LNCS).Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
}
TY - GEN
T1 - Composite pattern discovery for PCR application
AU - Angelov, Stanislav
AU - Inenaga, Shunsuke
PY - 2005/12/1
Y1 - 2005/12/1
N2 - We consider the problem of finding pairs of short patterns such that, in a given input sequence of length n, the distance between each pair's patterns is at least α. The problem was introduced in [1] and is motivated by the optimization of multiplexed nested PCR. We study algorithms for the following two cases; the special case when the two patterns in the pair are required to have the same length, and the more general case when the patterns can have different lengths. For the first case we present an O(αn log log n) time and O(n) space algorithm, and for the general case we give an O(αn log n) time and O(n) space algorithm. The algorithms work for any alphabet size and use asymptotically less space than the algorithms presented in [1]. For alphabets of constant size we also give an O(n√n log2 n) time algorithm for the general case. We demonstrate that the algorithms perform well in practice and present our findings for the human genome. In addition, we study an extended version of the problem where patterns in the pair occur at certain positions at a distance at most α, but do not occur α-close anywhere else, in the input sequence.
AB - We consider the problem of finding pairs of short patterns such that, in a given input sequence of length n, the distance between each pair's patterns is at least α. The problem was introduced in [1] and is motivated by the optimization of multiplexed nested PCR. We study algorithms for the following two cases; the special case when the two patterns in the pair are required to have the same length, and the more general case when the patterns can have different lengths. For the first case we present an O(αn log log n) time and O(n) space algorithm, and for the general case we give an O(αn log n) time and O(n) space algorithm. The algorithms work for any alphabet size and use asymptotically less space than the algorithms presented in [1]. For alphabets of constant size we also give an O(n√n log2 n) time algorithm for the general case. We demonstrate that the algorithms perform well in practice and present our findings for the human genome. In addition, we study an extended version of the problem where patterns in the pair occur at certain positions at a distance at most α, but do not occur α-close anywhere else, in the input sequence.
UR - http://www.scopus.com/inward/record.url?scp=33646754225&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=33646754225&partnerID=8YFLogxK
U2 - 10.1007/11575832_19
DO - 10.1007/11575832_19
M3 - Conference contribution
SN - 3540297405
SN - 9783540297406
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 167
EP - 178
BT - String Processing and Information Retrieval - 12th International Conference, SPIRE 2005, Proceedings
ER -