Efficient Encoding/Decoding of Irreducible Words for Codes Correcting Tandem Duplications

Tandem duplication is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain et al. (2017) proposed the study of codes that correct tandem duplications. All code constructions are based on irreducible...

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Vydáno v:2018 IEEE International Symposium on Information Theory (ISIT) s. 2406 - 2410
Hlavní autoři: Chee, Yeow Meng, Chrisnata, Johan, Kiah, Han Mao, Nguyen, Tuan Thanh
Médium: Konferenční příspěvek
Jazyk:angličtina
Vydáno: IEEE 01.06.2018
Témata:
Codes
DNA
Encoding
Genetic communication
Organisms
ISSN:2157-8117
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Shrnutí:Tandem duplication is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain et al. (2017) proposed the study of codes that correct tandem duplications. All code constructions are based on irreducible words. We study efficient encoding/decoding methods for irreducible words. First, we describe an (\ell,\ m) -finite state encoder and show that when m=\Theta(1/\epsilon) and \ell=\Theta(1/\epsilon) , the encoder has rate that is \epsilon away from the optimal. Next, we provide ranking/unranking algorithms for irreducible words and modify the algorithms to reduce the space requirements for the finite state encoder.
ISSN:2157-8117
DOI:10.1109/ISIT.2018.8437789