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Two combinatorial optimization problems for SNP discovery using base-specific cleavage and mass spectrometry
BACKGROUND: The 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 v...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3521188/ https://www.ncbi.nlm.nih.gov/pubmed/23282116 http://dx.doi.org/10.1186/1752-0509-6-S2-S5 |
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author | Chen, Xin Wu, Qiong Sun, Ruimin Zhang, Louxin |
author_facet | Chen, Xin Wu, Qiong Sun, Ruimin Zhang, Louxin |
author_sort | Chen, Xin |
collection | PubMed |
description | BACKGROUND: The 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. RESULTS: 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 [Formula: see text] , 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 [Formula: see text] , 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 [Formula: see text] problem and also show that the [Formula: see text] problem is NP-hard by a reduction from a restricted variation of the 3-partition problem. CONCLUSIONS: 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. |
format | Online Article Text |
id | pubmed-3521188 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-35211882012-12-14 Two combinatorial optimization problems for SNP discovery using base-specific cleavage and mass spectrometry Chen, Xin Wu, Qiong Sun, Ruimin Zhang, Louxin BMC Syst Biol Proceedings BACKGROUND: The 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. RESULTS: 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 [Formula: see text] , 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 [Formula: see text] , 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 [Formula: see text] problem and also show that the [Formula: see text] problem is NP-hard by a reduction from a restricted variation of the 3-partition problem. CONCLUSIONS: 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. BioMed Central 2012-12-12 /pmc/articles/PMC3521188/ /pubmed/23282116 http://dx.doi.org/10.1186/1752-0509-6-S2-S5 Text en Copyright ©2012 Chen et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 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. |
spellingShingle | Proceedings Chen, Xin Wu, Qiong Sun, Ruimin Zhang, Louxin Two combinatorial optimization problems for SNP discovery using base-specific cleavage and mass spectrometry |
title | Two combinatorial optimization problems for SNP discovery using base-specific cleavage and mass spectrometry |
title_full | Two combinatorial optimization problems for SNP discovery using base-specific cleavage and mass spectrometry |
title_fullStr | Two combinatorial optimization problems for SNP discovery using base-specific cleavage and mass spectrometry |
title_full_unstemmed | Two combinatorial optimization problems for SNP discovery using base-specific cleavage and mass spectrometry |
title_short | Two combinatorial optimization problems for SNP discovery using base-specific cleavage and mass spectrometry |
title_sort | two combinatorial optimization problems for snp discovery using base-specific cleavage and mass spectrometry |
topic | Proceedings |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3521188/ https://www.ncbi.nlm.nih.gov/pubmed/23282116 http://dx.doi.org/10.1186/1752-0509-6-S2-S5 |
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