Please use this identifier to cite or link to this item:
https://hdl.handle.net/10356/105219
Title: | Two combinatorial optimization problems for SNP discovery using base-specific cleavage and mass spectrometry | Authors: | Chen, Xin Wu, Qiong Sun, Ruimin Zhang, Louxin |
Keywords: | DRNTU::Science::Biological sciences::Biomathematics | Issue Date: | 2012 | Source: | Chen, 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). | Series/Report no.: | BMC systems biology | Abstract: | 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. 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. | URI: | https://hdl.handle.net/10356/105219 http://hdl.handle.net/10220/16762 |
ISSN: | 1752-0509 | DOI: | 10.1186/1752-0509-6-S2-S5 | Schools: | School of Physical and Mathematical Sciences | 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. | Fulltext Permission: | open | Fulltext Availability: | With Fulltext |
Appears in Collections: | SPMS Journal Articles |
Files in This Item:
File | Description | Size | Format | |
---|---|---|---|---|
Two combinatorial optimization problems for SNP.pdf | 668.31 kB | Adobe PDF | View/Open |
SCOPUSTM
Citations
20
8
Updated on Mar 26, 2024
Web of ScienceTM
Citations
50
2
Updated on Oct 31, 2023
Page view(s) 50
466
Updated on Mar 28, 2024
Download(s) 20
173
Updated on Mar 28, 2024
Google ScholarTM
Check
Altmetric
Items in DR-NTU are protected by copyright, with all rights reserved, unless otherwise indicated.