PairMotif: A new pattern-driven algorithm for planted (l, d) DNA motif search.
PairMotif: A new pattern-driven algorithm for planted (l, d) DNA motif search.
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PairMotif：一种新的模式驱动算法，用于植入 (l, d) DNA 基序搜索。
DOI：
10.1371/journal.pone.0048442
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Guo H
中科院分区：
文献类型：
--
作者：
Yu Q;Huo H;Zhang Y;Guo H
Motif search is a fundamental problem in bioinformatics with an important application in locating transcription factor binding sites (TFBSs) in DNA sequences. The exact algorithms can report all (l, d) motifs and find the best one under a specific objective function. However, it is still a challenging task to identify weak motifs, since either a large amount of memory or execution time is required by current exact algorithms. A new exact algorithm, PairMotif, is proposed for planted (l, d) motif search (PMS) in this paper. To effectively reduce both candidate motifs and scanned l-mers, multiple pairs of l-mers with relatively large distances are selected from input sequences to restrict the search space. Comparisons with several recently proposed algorithms show that PairMotif requires less storage space and runs faster on most PMS instances. Particularly, among the algorithms compared, only PairMotif can solve the weak instance (27, 9) within 10 hours. Moreover, the performance of PairMotif is stable over the sequence length, which allows it to identify motifs in longer sequences. For the real biological data, experimental results demonstrate the validity of the proposed algorithm.
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影响因子：
3.7
作者：
Miller AK;Print CG;Nielsen PM;Crampin EJ
通讯作者：
Crampin EJ
影响因子：
5.8
作者：
Fratkin, Eugene;Naughton, Brian T.;Batzoglou, Serafim
通讯作者：
Batzoglou, Serafim
DOI：
10.1007/11682462_69
发表时间：
2006-01-01
期刊：
LATIN 2006: THEORETICAL INFORMATICS
影响因子：
--
作者：
Pisanti, N;Carvalho, AM;Sagot, MR
通讯作者：
Sagot, MR
影响因子：
14.9
作者：
Bulyk, ML;Johnson, PLF;Church, GM
通讯作者：
Church, GM
影响因子：
3
作者：
Kuksa PP;Pavlovic V
通讯作者：
Pavlovic V