An optimization approach to the reconstruction of positional DNA sequencing by hybridization with errors

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.