dc.contributor.authorChen, Xin
dc.contributor.authorWu, Qiong
dc.contributor.authorSun, Ruimin
dc.contributor.authorZhang, Louxin
dc.date.accessioned2013-10-24T06:01:24Z
dc.date.available2013-10-24T06:01:24Z
dc.date.copyright2012en_US
dc.date.issued2012
dc.identifier.citationChen, X., Wu, Q., Sun, R., & Zhang, L. (2012). Two combinatorial optimization problems for SNP discovery using base-specific cleavage and mass spectrometry. BMC Systems Biology, 6(Suppl 2).en_US
dc.identifier.issn1752-0509en_US
dc.identifier.urihttp://hdl.handle.net/10220/16762
dc.description.abstractThe discovery of single-nucleotide polymorphisms (SNPs) has important implications in a variety of genetic studies on human diseases and biological functions. One valuable approach proposed for SNP discovery is based on base-specific cleavage and mass spectrometry. However, it is still very challenging to achieve the full potential of this SNP discovery approach. In this study, we formulate two new combinatorial optimization problems. While both problems are aimed at reconstructing the sample sequence that would attain the minimum number of SNPs, they search over different candidate sequence spaces. The first problem, denoted as SNP - MS P , limits its search to sequences whose in silico predicted mass spectra have all their signals contained in the measured mass spectra. In contrast, the second problem, denoted as SNP - MS Q , limits its search to sequences whose in silico predicted mass spectra instead contain all the signals of the measured mass spectra. We present an exact dynamic programming algorithm for solving the SNP - MS P problem and also show that the SNP - MS Q problem is NP-hard by a reduction from a restricted variation of the 3-partition problem. We believe that an efficient solution to either problem above could offer a seamless integration of information in four complementary base-specific cleavage reactions, thereby improving the capability of the underlying biotechnology for sensitive and accurate SNP discovery.en_US
dc.description.sponsorshipNMRC (Natl Medical Research Council, S’pore)
dc.language.isoenen_US
dc.relation.ispartofseriesBMC systems biologyen_US
dc.rights© 2012 Chen et al.; licensee BioMed Central Ltd. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.en_US
dc.subjectDRNTU::Science::Biological sciences::Biomathematics
dc.titleTwo combinatorial optimization problems for SNP discovery using base-specific cleavage and mass spectrometryen_US
dc.typeJournal Article
dc.contributor.schoolSchool of Physical and Mathematical Sciencesen_US
dc.identifier.doihttp://dx.doi.org/10.1186/1752-0509-6-S2-S5
dc.description.versionPublished version
dc.identifier.rims168381


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