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

Author

Orth, John ; Houghten, Sheridan

Author_Institution

Dept. of Comput. Sci., Brock Univ., St. Catharines, ON, Canada

fYear

2011

fDate

11-15 April 2011

Firstpage

1

Lastpage

7

Abstract

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.

Keywords

DNA; biology computing; error correction codes; optimisation; DNA error correcting codes; biological restrictions; codewords; embeddable markers; salmon algorithm optimization; search metaheuristic; sequencing errors; Algorithm design and analysis; Biological information theory; Computer science; Error correction codes; Genetic algorithms; Tuning;

fLanguage

English

Publisher

ieee

Conference_Titel

Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2011 IEEE Symposium on

Conference_Location

Paris

Print_ISBN

978-1-4244-9896-3

Type

conf

DOI

10.1109/CIBCB.2011.5948476

Filename

5948476