Natural Data Storage: A Review on sending Information from now to then via Nature <s> Error correction in DNA based information systems <s> For very long-term storage and retrieval, encode information as artificial DNA strands and insert into living hosts. As vectors, bacteria, even some bugs and weeds, might be good for hundreds of millions of years. <s> BIB001 </s> Natural Data Storage: A Review on sending Information from now to then via Nature <s> Error correction in DNA based information systems <s> The time is approaching when information can be written into DNA. This tutorial work surveys the methods for designing code words using DNA, and proposes a simple code that avoids unwanted hybridization in the presence of shift and concatenation of DNA words and their complements. <s> BIB002 </s> Natural Data Storage: A Review on sending Information from now to then via Nature <s> Error correction in DNA based information systems <s> Three codes are reported for storing written information in DNA. We refer to these codes as the Huffman code, the comma code and the alternating code. The Huffman code was devised using Huffman's algorithm for constructing economical codes. The comma code uses a single base to punctuate the message, creating an automatic reading frame and DNA which is obviously artificial. The alternating code comprises an alternating sequence of purines and pyrimidines, again creating DNA that is clearly artificial. The Huffman code would be useful for routine, short-term storage purposes, supposing – not unrealistically – that very fast methods for assembling and sequencing large pieces of DNA can be developed. The other two codes would be better suited to archiving data over long periods of time (hundreds to thousands of years). <s> BIB003 </s> Natural Data Storage: A Review on sending Information from now to then via Nature <s> Error correction in DNA based information systems <s> Information encoding and processing in DNA has proved to be an important problem for biomolecular computing, including the well studied codeword design problem. A lower bound is established for the capacity of DNA to encode information using a combinatorial model of DNA homology given by the so-called h-distance. This bound decreases exponentially with a parameter r that roughly codes for stringency in reaction conditions. We further introduce a new family of near-optimal codeword sets, so-called shuffle codes. This construction, which is optimal in terms of efficiency, can also be used to produce set of codewords with a given constant GC-content. These codes yield estimates of the capacity of DNA oligonucleotides to store abiotic information in DNA arrays as defined in [11]. Finally, we discuss the sensitivity of the corresponding DNA chip encodings to store and discriminate inputs, including the regions of maximum discrimination and uncertainty. <s> BIB004 </s> Natural Data Storage: A Review on sending Information from now to then via Nature <s> Error correction in DNA based information systems <s> A simple, practical method to watermark short trademarks or signatures into genomic DNA is introduced. Since the marking method is biologically innocuous, it can be applied to all commercialized bacteria to help establish brand names for the engineered strains and to resolve legal disputes regarding gene-related patents. The first such strain of Bacillus subtilis is engineered and is ready to be distributed. <s> BIB005 </s> Natural Data Storage: A Review on sending Information from now to then via Nature <s> Error correction in DNA based information systems <s> Data-encoding synthetic DNA, inserted into the genome of a living organism, is thought to be more robust than the current media. Because the living genome is duplicated and copied into new generations, one of the merits of using DNA material is long-term data storage within heritable media. A disadvantage of this approach is that encoded data can be unexpectedly broken by mutation, deletion, and insertion of DNA, which occurs naturally during evolution and prolongation, or laboratory experiments. For this reason, several information theory-based approaches have been developed as an error check of broken DNA data in order to achieve data durability. These approaches cannot efficiently recover badly damaged data-encoding DNA. We recently developed a DNA data-storage approach based on the multiple sequence alignment method to achieve a high level of data durability. In this paper, we overview this technology and discuss strategies for optimal application of this approach. <s> BIB006 </s> Natural Data Storage: A Review on sending Information from now to then via Nature <s> Error correction in DNA based information systems <s> An improved Huffman coding method for information storage in DNA is described. The method entails the utilization of modified unambiguous base assignment that enables efficient coding of characters. A plasmid-based library with efficient and reliable information retrieval and assembly with uniquely designed primers is described. We illustrate our approach by synthesis of DNA that encodes text, images, and music, which could easily be retrieved by DNA sequencing using the specific primers. The method is simple and lends itself to automated information retrieval. <s> BIB007 </s> Natural Data Storage: A Review on sending Information from now to then via Nature <s> Error correction in DNA based information systems <s> A number of methods have been proposed over the last decade for embedding information within deoxyribonucleic acid (DNA). Since a DNA sequence is conceptually equivalent to a unidim ensional digital signal, DNA data embedding (diversely called DNA watermarking or DNA steganograph y) can be seen either as a traditional communications problem or as an instance of communications with side information at the encoder, similar to data hiding. These two cases correspond to the use of noncoding o r coding DNA hosts, which, respectively, denote DNA segments that cannot or can be translated into proteins. A limit ation of existing DNA data embedding methods is that none of them have been designed according to optim al coding principles. It is not possible either to evaluate how close to optimality these methods are without deter mining the Shannon capacity of DNA data embedding. This is the main topic studied in this paper, where we consid er that DNA sequences may be subject to substitution, insertion, and deletion mutations. <s> BIB008 </s> Natural Data Storage: A Review on sending Information from now to then via Nature <s> Error correction in DNA based information systems <s> The goal of DNA data embedding is to enable robust encoding of non-genetic information in DNA. This field straddles the areas of bioinformatics and digital communications, since DNA mutations can be seen as akin to a noisy channel from the point of view of information encoding. In this paper we present two algorithms which, building on a variant of a method proposed by Yachie et al., rely on repetition coding to effectively counteract the impact that mutations have on an embedded message. The algorithms are designed for resynchronising multiple, originally identical, information encoded DNA sequences, embedded within non-coding DNA (ncDNA) sections of a host genome. They use both BLAST and MUSCLE algorithms to accomplish this. Bit error rates at the decoder are established for mutations rates accumulated over a number of generations of the host organism. The empirical results obtained are compared to a theoretical bound for optimal decoding. <s> BIB009 </s> Natural Data Storage: A Review on sending Information from now to then via Nature <s> Error correction in DNA based information systems <s> Digital production, transmission and storage have revolutionized how we access and use information but have also made archiving an increasingly complex task that requires active, continuing maintenance of digital media. This challenge has focused some interest on DNA as an attractive target for information storage because of its capacity for high-density information encoding, longevity under easily achieved conditions and proven track record as an information bearer. Previous DNA-based information storage approaches have encoded only trivial amounts of information or were not amenable to scaling-up, and used no robust error-correction and lacked examination of their cost-efficiency for large-scale information archival. Here we describe a scalable method that can reliably store more information than has been handled before. We encoded computer files totalling 739 kilobytes of hard-disk storage and with an estimated Shannon information of 5.2 × 10(6) bits into a DNA code, synthesized this DNA, sequenced it and reconstructed the original files with 100% accuracy. Theoretical analysis indicates that our DNA-based storage scheme could be scaled far beyond current global information volumes and offers a realistic technology for large-scale, long-term and infrequently accessed digital archiving. In fact, current trends in technological advances are reducing DNA synthesis costs at a pace that should make our scheme cost-effective for sub-50-year archiving within a decade. <s> BIB010 </s> Natural Data Storage: A Review on sending Information from now to then via Nature <s> Error correction in DNA based information systems <s> Information, such as text printed on paper or images projected onto microfilm, can survive for over 500 years. However, the storage of digital information for time frames exceeding 50 years is challenging. Here we show that digital information can be stored on DNA and recovered without errors for considerably longer time frames. To allow for the perfect recovery of the information, we encapsulate the DNA in an inorganic matrix, and employ error-correcting codes to correct storage-related errors. Specifically, we translated 83 kB of information to 4991 DNA segments, each 158 nucleotides long, which were encapsulated in silica. Accelerated aging experiments were performed to measure DNA decay kinetics, which show that data can be archived on DNA for millennia under a wide range of conditions. The original information could be recovered error free, even after treating the DNA in silica at 70 °C for one week. This is thermally equivalent to storing information on DNA in central Europe for 2000 years. <s> BIB011
There are different types of errors associated with DNA data storage systems which are physical errors and genetic errors. Physical errors occur during synthesis and sequencing of DNA and genetic errors are caused by mutations which occurs naturally during evolution and prolongation. Error can be insertion, deletion or substitution of single base in DNA sequences. Substitution of single base can be considered as bit flip errors. Other type of error can be deletion of bunch of DNA nucleotides categorized as burst error. Reading error rates ranges from 1-3 % while writing error has error rates upto 15 %. Error models proposed so far have focus on physical errors like substitution and deletion of oligonucleotides BIB009  but no work has been done on insertion error model. There are three basic codes for storing data in DNA BIB002 ] which are Huffman code, comma code and the alternating code. Although comma-free code and alternate codes are robust and has ability to correct against small-scale damage such as DNA point mutations, this cannot recover broken data block from the data-encoded DNA region. This breakpoints can be corrected by Huffman coding BIB006 . The DNA encoding by Huffman codes developed the Huffman coding method  ] is uniquely decodable. In this method, the probabilities of the symbol is considered (here the symbols are the English Alphabet). The least probabilities symbols are added to generate the next symbol and the process is repeated until we get the unique codes for all the symbols. For base 2 Huffman code, the least two probabilities are added and reduced two generate compact code until all the symbols are coded with code 0 and 1. Likewise for base 3 and 4 base Huffman, least three and least four probabilities symbols respectively are reduced to compact code. The Huffman code described in BIB003 ], used the probabilities of the English alphabet. According to this the highest occurred letter e has single base code and the least occurred z has code length of 5 bases. For this base 2 Huffman code, the two least frequencies are summed up to give compact code. The codes are assigned by varying the wobble position (third position of the codon) for the alphabet with similar probabilities. Average code length of the code is 2.2 which is shorter compare to other codes. The drawback of the method is that it do not include symbols and other characters. The improved Huffman code using all the English alphabets and special character was described using specific base assignment with uniquely designed primer sequences BIB007 . The remarkable Huffman method was used by Goldman and his colleagues BIB010 ] with error correction techniques. In recent year, DNA storage channel was described by Han Mao Kiah et al; in which they represented reading and writing errors during DNA data storage as profile vectors and designed a family of error correcting codes for synthesis and sequencing errors  . They developed a codeword designed technique that resulted in the codes at sufficiently large distance that makes it best possible for error correction. DNA has essential property for long term archival of data compare to digital storage devices. To witness long term storage of DNA and improve the DNA stability, researchers have develop chemical based BIB011 method to encapsulate DNA into glass sphere and preserve it from environmental damage for long term archival. They used very prominent error correcting code Reed Solomon codes, which are used in digital storage devices like CD, DVD, to implement two layer of encoding one at DNA chunk level and other at synthesis and sequencing of DNA. This method can correct burst error. Recently re-writable DNA based data storage systems is proposed in  , in which they used unique addressing scheme by which data can be randomly accessed unlike previous techniques in which random access of data was not possible. BIB004 in terms of hybridization model. He stated that it is very difficult to estimate the Shannon capacity for DNA of given length to store data. He considered hybridization can occur only if set of DNA are at some distance with parameter τ for the reaction stringency and gave the lower bound on DNA capacity to store the a-biotic data. Other models considered mutation in DNA sequences to estimate the Shannon capacity. Capacity of DNA under the substitution BIB008 ], insertion and deletion error  ] was proposed by F. Balado. Considering encoding of data in non coding or coding region of genome, upper limit of Shannon capacity for amount of data stored in DNA under the error rate was specified. Upper bound for the DNA storage capacity without error is 2 bits per base. All the encoding methods used for embedding data in DNA have achieve Shannon information density ranging from 2 bits per base BIB001 BIB005 . Goldman achieve 1.58 bits per base Shannon information for each DNA string. There are many low hanging fruits for designing the optimal capacity achieving codes for DNA storage with better code rate and length of DNA chunk.