Show simple item record

dc.contributor.authorHaughton, David
dc.contributor.authorBalado, Félix
dc.date.accessioned2013-07-04T12:49:13Z
dc.date.available2013-07-04T12:49:13Z
dc.date.issued2013-04-09
dc.identifier.citationBMC Bioinformatics. 2013 Apr 09;14(1):121
dc.identifier.urihttp://dx.doi.org/10.1186/1471-2105-14-121
dc.identifier.urihttp://hdl.handle.net/10147/295222
dc.description.abstractAbstract Background In recent times, the application of deoxyribonucleic acid (DNA) has diversified with the emergence of fields such as DNA computing and DNA data embedding. DNA data embedding, also known as DNA watermarking or DNA steganography, aims to develop robust algorithms for encoding non-genetic information in DNA. Inherently DNA is a digital medium whereby the nucleotide bases act as digital symbols, a fact which underpins all bioinformatics techniques, and which also makes trivial information encoding using DNA straightforward. However, the situation is more complex in methods which aim at embedding information in the genomes of living organisms. DNA is susceptible to mutations, which act as a noisy channel from the point of view of information encoded using DNA. This means that the DNA data embedding field is closely related to digital communications. Moreover it is a particularly unique digital communications area, because important biological constraints must be observed by all methods. Many DNA data embedding algorithms have been presented to date, all of which operate in one of two regions: non-coding DNA (ncDNA) or protein-coding DNA (pcDNA). Results This paper proposes two novel DNA data embedding algorithms jointly called BioCode, which operate in ncDNA and pcDNA, respectively, and which comply fully with stricter biological restrictions. Existing methods comply with some elementary biological constraints, such as preserving protein translation in pcDNA. However there exist further biological restrictions which no DNA data embedding methods to date account for. Observing these constraints is key to increasing the biocompatibility and in turn, the robustness of information encoded in DNA. Conclusion The algorithms encode information in near optimal ways from a coding point of view, as we demonstrate by means of theoretical and empirical (in silico) analyses. Also, they are shown to encode information in a robust way, such that mutations have isolated effects. Furthermore, the preservation of codon statistics, while achieving a near-optimum embedding rate, implies that BioCode pcDNA is also a near-optimum first-order steganographic method.
dc.titleBioCode: Two biologically compatible Algorithms for embedding data in non-coding and coding regions of DNA
dc.typeJournal Article
dc.language.rfc3066en
dc.rights.holderDavid Haughton et al.; licensee BioMed Central Ltd.
dc.description.statusPeer Reviewed
dc.date.updated2013-07-01T11:09:29Z
refterms.dateFOA2018-08-23T06:04:38Z
html.description.abstractAbstract Background In recent times, the application of deoxyribonucleic acid (DNA) has diversified with the emergence of fields such as DNA computing and DNA data embedding. DNA data embedding, also known as DNA watermarking or DNA steganography, aims to develop robust algorithms for encoding non-genetic information in DNA. Inherently DNA is a digital medium whereby the nucleotide bases act as digital symbols, a fact which underpins all bioinformatics techniques, and which also makes trivial information encoding using DNA straightforward. However, the situation is more complex in methods which aim at embedding information in the genomes of living organisms. DNA is susceptible to mutations, which act as a noisy channel from the point of view of information encoded using DNA. This means that the DNA data embedding field is closely related to digital communications. Moreover it is a particularly unique digital communications area, because important biological constraints must be observed by all methods. Many DNA data embedding algorithms have been presented to date, all of which operate in one of two regions: non-coding DNA (ncDNA) or protein-coding DNA (pcDNA). Results This paper proposes two novel DNA data embedding algorithms jointly called BioCode, which operate in ncDNA and pcDNA, respectively, and which comply fully with stricter biological restrictions. Existing methods comply with some elementary biological constraints, such as preserving protein translation in pcDNA. However there exist further biological restrictions which no DNA data embedding methods to date account for. Observing these constraints is key to increasing the biocompatibility and in turn, the robustness of information encoded in DNA. Conclusion The algorithms encode information in near optimal ways from a coding point of view, as we demonstrate by means of theoretical and empirical (in silico) analyses. Also, they are shown to encode information in a robust way, such that mutations have isolated effects. Furthermore, the preservation of codon statistics, while achieving a near-optimum embedding rate, implies that BioCode pcDNA is also a near-optimum first-order steganographic method.


Files in this item

Thumbnail
Name:
1471-2105-14-121.xml
Size:
190.7Kb
Format:
XML
Thumbnail
Name:
1471-2105-14-121.pdf
Size:
1.465Mb
Format:
PDF
Thumbnail
Name:
1471-2105-14-121-S1.PDF
Size:
212.7Kb
Format:
PDF

This item appears in the following Collection(s)

Show simple item record