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- Publisher Website: 10.1109/BIBE.2006.253318
- Scopus: eid_2-s2.0-34347342058
Conference Paper: Discovering DNA motifs with nucleotide dependency
Title | Discovering DNA motifs with nucleotide dependency |
---|---|
Authors | |
Issue Date | 2006 |
Citation | Proceedings - Sixth Ieee Symposium On Bioinformatics And Bioengineering, Bibe 2006, 2006, p. 70-77 How to Cite? |
Abstract | The problem of finding motifs of binding sites is very important to the understanding of gene regulatory networks. Motifs are generally represented by matrices (PWM or PSSM) or strings. However, these representations cannot model biological binding sites well because they fail to capture nucleotide interdependence. It has been pointed out by many researchers that the nucleotides of the DNA binding site cannot be treated independently, e.g. the binding of zinc finger in proteins. In this paper, a new representation called Scored Position Specific Pattern (SPSP), which is a generalization of the matrix and string representations, is introduced which takes into consideration the dependent occurrences of neighboring nucleotides. Even though the problem of finding the optimal motif in SPSP representation is proved to be NP-hard, we introduce a heuristic algorithm called SPSP-Finder, which can effectively find optimal motifs in most simulated cases and some real cases for which existing popular motiffinding software, such as MEME and AlignACE, fail. © 2006 IEEE. |
Persistent Identifier | http://hdl.handle.net/10722/93375 |
References |
DC Field | Value | Language |
---|---|---|
dc.contributor.author | Leung, HCM | en_HK |
dc.contributor.author | Chin, FYL | en_HK |
dc.date.accessioned | 2010-09-25T14:59:11Z | - |
dc.date.available | 2010-09-25T14:59:11Z | - |
dc.date.issued | 2006 | en_HK |
dc.identifier.citation | Proceedings - Sixth Ieee Symposium On Bioinformatics And Bioengineering, Bibe 2006, 2006, p. 70-77 | en_HK |
dc.identifier.uri | http://hdl.handle.net/10722/93375 | - |
dc.description.abstract | The problem of finding motifs of binding sites is very important to the understanding of gene regulatory networks. Motifs are generally represented by matrices (PWM or PSSM) or strings. However, these representations cannot model biological binding sites well because they fail to capture nucleotide interdependence. It has been pointed out by many researchers that the nucleotides of the DNA binding site cannot be treated independently, e.g. the binding of zinc finger in proteins. In this paper, a new representation called Scored Position Specific Pattern (SPSP), which is a generalization of the matrix and string representations, is introduced which takes into consideration the dependent occurrences of neighboring nucleotides. Even though the problem of finding the optimal motif in SPSP representation is proved to be NP-hard, we introduce a heuristic algorithm called SPSP-Finder, which can effectively find optimal motifs in most simulated cases and some real cases for which existing popular motiffinding software, such as MEME and AlignACE, fail. © 2006 IEEE. | en_HK |
dc.language | eng | en_HK |
dc.relation.ispartof | Proceedings - Sixth IEEE Symposium on BioInformatics and BioEngineering, BIBE 2006 | en_HK |
dc.title | Discovering DNA motifs with nucleotide dependency | en_HK |
dc.type | Conference_Paper | en_HK |
dc.identifier.email | Leung, HCM:cmleung2@cs.hku.hk | en_HK |
dc.identifier.email | Chin, FYL:chin@cs.hku.hk | en_HK |
dc.identifier.authority | Leung, HCM=rp00144 | en_HK |
dc.identifier.authority | Chin, FYL=rp00105 | en_HK |
dc.description.nature | link_to_subscribed_fulltext | - |
dc.identifier.doi | 10.1109/BIBE.2006.253318 | en_HK |
dc.identifier.scopus | eid_2-s2.0-34347342058 | en_HK |
dc.identifier.hkuros | 128853 | en_HK |
dc.relation.references | http://www.scopus.com/mlt/select.url?eid=2-s2.0-34347342058&selection=ref&src=s&origin=recordpage | en_HK |
dc.identifier.spage | 70 | en_HK |
dc.identifier.epage | 77 | en_HK |
dc.identifier.scopusauthorid | Leung, HCM=35233742700 | en_HK |
dc.identifier.scopusauthorid | Chin, FYL=7005101915 | en_HK |
dc.identifier.citeulike | 4284508 | - |