An optimization approach to the reconstruction of positional DNA sequencing by hybridization with errors |
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Authors: | Ji-Hong Zhang Ling-Yun Wu Yu-Ying Zhao Xiang-Sun Zhang |
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Institution: | 1. School of Economics and Managements, Tsinghua University, Beijing 100084, China;2. Center of Bioinformatics, Academy of Mathematics and Systems Science, CAS, Beijing 100080, China;3. School of International Business, Beijing Foreign Studies University, Beijing 100089, China |
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Abstract: | Positional DNA sequencing by hybridization (PSBH) is a recently proposed enhancement of DNA sequencing by hybridization (SBH, potentially a powerful alternative to the DNA sequencing by gel electrophoresis). It has been discussed in many papers and applied to large scale sequencing by hybridization. However, the computational part of PSBH reconstruction is a difficult problem, especially for the occurrence of hybridization errors. So far the problem has not been solved well. Taking PSBH as a combinatorial optimization problem, a novel reconstruction approach to PSBH is presented in this paper. The proposed approach accepts both the negative and positive errors and can greatly reduce ambiguities in the reconstruction of PSBH. The computational experiment shows that our algorithm works satisfactorily and correctly on the test data, especially for the positive errors and k-tuple repetitions. |
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Keywords: | Positional sequencing by hybridization Reconstruction of DNA fragment Positive errors and negative errors Dynamic programming Branch and bound algorithm |
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