On the synthesis of DNA error correcting codes |
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| Authors: | Daniel Ashlock Sheridan K Houghten Joseph Alexander Brown John Orth |
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| Institution: | 1. Department of Mathematics and Statistics, University of Guelph, Guelph, Ontario, N1G 2W1, Canada;2. Department of Computer Science, Brock University, St. Catharines, Ontario, L2S 3A1, Canada;3. School of Computer Science, University of Guelph, Guelph, Ontario, N1G 2W1, Canada;4. Department of Computer Science, Brock University, St. Catharines, Ontario, L2S 3A1, Canada |
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| Abstract: | DNA error correcting codes over the edit metric consist of embeddable markers for sequencing projects that are tolerant of sequencing errors. When a genetic library has multiple sources for its sequences, use of embedded markers permit tracking of sequence origin. This study compares different methods for synthesizing DNA error correcting codes. A new code-finding technique called the salmon algorithm is introduced and used to improve the size of best known codes in five difficult cases of the problem, including the most studied case: length six, distance three codes. An updated table of the best known code sizes with 36 improved values, resulting from three different algorithms, is presented. Mathematical background results for the problem from multiple sources are summarized. A discussion of practical details that arise in application, including biological design and decoding, is also given in this study. |
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| Keywords: | Evolutionarycomputation Bioinformatics Representation Error correcting code Nucleic acids Next-gen sequencing |
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