PairMotif: A New Pattern-Driven Algorithm for Planted (l, d) DNA Motif Search
Identifieur interne : 002225 ( Main/Exploration ); précédent : 002224; suivant : 002226PairMotif: A New Pattern-Driven Algorithm for Planted (l, d) DNA Motif Search
Auteurs : Qiang Yu ; Hongwei Huo ; Yipu Zhang ; Hongzhi GuoSource :
- PLoS ONE [ 1932-6203 ] ; 2012.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : DNA.
- chemical , metabolism : Transcription Factors.
- methods : Computational Biology.
- Algorithms, Binding Sites, Computer Simulation, Nucleotide Motifs, Pattern Recognition, Automated, Software.
Abstract
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 (
Url:
DOI: 10.1371/journal.pone.0048442
PubMed: 23119020
PubMed Central: 3485246
Affiliations:
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Le document en format XML
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, <italic>d</italic>
) DNA Motif Search</title>
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<term>Computer Simulation</term>
<term>DNA (chemistry)</term>
<term>Nucleotide Motifs</term>
<term>Pattern Recognition, Automated</term>
<term>Software</term>
<term>Transcription Factors (metabolism)</term>
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<keywords scheme="KwdFr" xml:lang="fr"><term>ADN ()</term>
<term>Algorithmes</term>
<term>Biologie informatique ()</term>
<term>Facteurs de transcription (métabolisme)</term>
<term>Logiciel</term>
<term>Motifs nucléotidiques</term>
<term>Reconnaissance automatique des formes</term>
<term>Simulation numérique</term>
<term>Sites de fixation</term>
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<term>Nucleotide Motifs</term>
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<front><div type="abstract" xml:lang="en"><p>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 (<italic>l</italic>
, <italic>d</italic>
) 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 (<italic>l</italic>
, <italic>d</italic>
) motif search (PMS) in this paper. To effectively reduce both candidate motifs and scanned <italic>l</italic>
-mers, multiple pairs of <italic>l</italic>
-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.</p>
</div>
</front>
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<tree><noCountry><name sortKey="Guo, Hongzhi" sort="Guo, Hongzhi" uniqKey="Guo H" first="Hongzhi" last="Guo">Hongzhi Guo</name>
<name sortKey="Huo, Hongwei" sort="Huo, Hongwei" uniqKey="Huo H" first="Hongwei" last="Huo">Hongwei Huo</name>
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