Construction of cyclic codes over 𝔽2+u𝔽2 for DNA computing

We construct codes over the ring F2 + uF2 with u 2 = 0 for use in DNA computing applications. The codes obtained satisfy the reverse complement constraint, the GC content constraint, and avoid the secondary structure. They are derived from cyclic reverse-complement codes over the ring F2 + uF2. We also construct an infinite family of BCH DNA codes.

[1]  P Shankar On BCH codes over arbitrary integer rings , 1979 .

[2]  R J Lipton,et al.  DNA solution of hard computational problems. , 1995, Science.

[3]  Graham H. Norton,et al.  On the Structure of Linear and Cyclic Codes over a Finite Chain Ring , 2000, Applicable Algebra in Engineering, Communication and Computing.

[4]  Yves Edel,et al.  Caps of order 3q2 in affine 4-space in characteristic 2 , 2004, Finite Fields Their Appl..

[5]  Ali Ghrayeb,et al.  Construction of cyclic codes over GF(4) for DNA computing , 2006, J. Frankl. Inst..

[6]  Navin Kashyap,et al.  On the Design of Codes for DNA Computing , 2005, WCC.

[7]  Parampalli Udaya,et al.  Decoding of cyclic codes over F2 + µF2 , 1999, IEEE Trans. Inf. Theory.

[8]  Masaaki Harada,et al.  Construction of optimal Type IV self-dual codes over F2+µF2 , 1999, IEEE Trans. Inf. Theory.

[9]  Richard J. Lipton,et al.  Breaking DES using a molecular computer , 1995, DNA Based Computers.

[10]  Steven T. Dougherty,et al.  Maximum distance codes over rings of order 4 , 2001, IEEE Trans. Inf. Theory.

[11]  Oliver D. King,et al.  Linear constructions for DNA codes , 2005, Theor. Comput. Sci..

[12]  Masud Mansuripur,et al.  Information storage and retrieval using macromolecules as storage media , 2003, Optical Data Storage.

[13]  Taher Abualrub,et al.  Cyclic codes over the rings Z2 + uZ2 and Z2 + uZ2 + u2Z2 , 2007, Des. Codes Cryptogr..

[14]  F. MacWilliams,et al.  The Theory of Error-Correcting Codes , 1977 .

[15]  Ronald W. Davis,et al.  Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar–coding strategy , 1996, Nature Genetics.

[16]  Masaaki Harada,et al.  Type II Codes Over F2 + u F2 , 1999, IEEE Trans. Inf. Theory.

[17]  Erik Winfree,et al.  On applying molecular computation to the data encryption standard , 1999, DNA Based Computers.

[18]  T. Aaron Gulliver,et al.  MDS and self-dual codes over rings , 2012, Finite Fields Their Appl..

[19]  Parampalli Udaya,et al.  Cyclic Codes and Self-Dual Codes Over F2 + uF2 , 1999, IEEE Trans. Inf. Theory.

[20]  R. Nussinov,et al.  Fast algorithm for predicting the secondary structure of single-stranded RNA. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[21]  René Schoof,et al.  Hecke operators and the weight distributions of certain codes , 1991, Journal of Combinatorial Theory.

[22]  Ali Ghrayeb,et al.  Cyclic DNA codes over the ring F2[u]/(u2-1) based on the deletion distance , 2009, J. Frankl. Inst..

[23]  N. J. A. Sloane,et al.  Modular andp-adic cyclic codes , 1995, Des. Codes Cryptogr..

[24]  Sergio R. López-Permouth,et al.  Cyclic and negacyclic codes over finite chain rings , 2004, IEEE Transactions on Information Theory.

[25]  Tor Helleseth,et al.  The minimum distance of the duals of binary irreducible cyclic codes , 2002, IEEE Trans. Inf. Theory.

[26]  Christine Bachoc,et al.  Applications of Coding Theory to the Construction of Modular Lattices , 1997, J. Comb. Theory A.

[27]  L M Adleman,et al.  Molecular computation of solutions to combinatorial problems. , 1994, Science.