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DNA assembly problem is well known for its high complexity both on biological and computational levels. Traditional laboratory approach to the problem, which involves DNA sequencing by hybridization or by gel electrophoresis, entails a lot of errors coming from experimental and algorithmic stages. DNA sequences constituting the traditional assembly input have lengths about a few hundreds of nucleotides...
Progress in bioengineering brought a new approach to DNA sequencing, which aim is to give highly reliable output of low cost and in short time. It is 454 sequencing, based on the pyrosequencing protocol, owned by 454 Life Sciences Corporation. Because of the sequences reliability this method is much better than others for assembly purposes. However, produced sequences are much shorter and there are...
We study the simplified partial digest problem (SPDP), which is a mathematical model for a new simplified partial digest method of genome mapping. This method is easy for laboratory implementation and robust with respect to the experimental errors. SPDP is NP-hard in the strong sense. We present an O(n2n) time enumerative algorithm (ENUM) and an O(n2q) time dynamic programming algorithm for the error-free...
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