Optimizing the Salmon Algorithm for the construction of DNA error-correcting codes

DNA error correcting codes over the edit metric can be used to correct sequencing errors. The codewords may be used as embeddable markers that allow one to track the origin of sequence data. The Salmon Algorithm is a search meta-heuristic inspired by the behaviour of salmon swimming upstream to spaw...

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Bibliographic Details
Published in2011 Symposium on Computational Intelligence in Bioinformatics and Computational Biology pp. 1 - 7
Main Authors Orth, J., Houghten, S.
Format Conference Proceeding
LanguageEnglish
Published IEEE 01.04.2011
Subjects
Algorithm design and analysis
Biological information theory
Computer science
Error correction codes
Genetic algorithms
Tuning
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ISBN9781424498963
1424498961
DOI10.1109/CIBCB.2011.5948476

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Summary:DNA error correcting codes over the edit metric can be used to correct sequencing errors. The codewords may be used as embeddable markers that allow one to track the origin of sequence data. The Salmon Algorithm is a search meta-heuristic inspired by the behaviour of salmon swimming upstream to spawn. This algorithm consists of a number of parameters, which we tune for the purpose of constructing DNA error correcting codes with a large number of codewords. Using this algorithm, several best known code sizes are improved. Construction of codes obeying biological restrictions is also discussed and the use of the Salmon Algorithm for this purpose is demonstrated.
ISBN:9781424498963
1424498961
DOI:10.1109/CIBCB.2011.5948476