On the synthesis of DNA error correcting codes

• Published in: BioSystems Vol. 110; no. 1; pp. 1 - 8
• Main Authors: Ashlock, Daniel, Houghten, Sheridan K., Brown, Joseph Alexander, Orth, John
• Format: Journal Article
• Language: English
• Published: Ireland Elsevier Ireland Ltd 01.10.2012
• Subjects: Algorithms; Bioinformatics; Computational Biology; DNA; DNA Repair; DNA Replication; Error correcting code; Evolutionarycomputation; Gene Library; monitoring; Next-gen sequencing; Nucleic acids; Representation; salmon; Representation; Error correcting code; Evolutionarycomputation; Nucleic acids; Next-gen sequencing; Bioinformatics
• ISSN: 0303-2647; 1872-8324; 1872-8324
• DOI: 10.1016/j.biosystems.2012.06.005

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.