Adaptable DNA Storage Coding: An Efficient Framework for Homopolymer Constraint Transitions
Many DNA storage codes take into account homopolymer and GC-content constraints. Still, these codes often need to meet additional practical database requirements, such as error correction and data queries, necessitating considerable financial and time investment in their training or design. As DNA s...
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| Vydané v: | IEEE access Ročník 12; s. 9976 - 9983 |
|---|---|
| Hlavní autori: | , |
| Médium: | Journal Article |
| Jazyk: | English |
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Piscataway
The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
2024
IEEE |
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| ISSN: | 2169-3536, 2169-3536 |
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| Abstract | Many DNA storage codes take into account homopolymer and GC-content constraints. Still, these codes often need to meet additional practical database requirements, such as error correction and data queries, necessitating considerable financial and time investment in their training or design. As DNA storage technologies, including sequencing and synthesis, continue to evolve rapidly, these codes may need to be retrained or redesigned to adapt to new constraints. In this study, we aim to design a method for adapting an existing DNA storage code to satisfy a new constraint, specifically concerning homopolymer variations. We present a simple and effective framework known as Transfer Coding, which directly maps DNA sequences from an original homopolymer constraint [Formula Omitted] to a new constraint [Formula Omitted]. This approach essentially combines the existing coding scheme with a Transfer encoder. The proposed method uses strategic base replacements to ensure compliance with constraints, achieving results close to the theoretical limit while keeping alterations to the original sequence minimal. |
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| AbstractList | Many DNA storage codes take into account homopolymer and GC-content constraints. Still, these codes often need to meet additional practical database requirements, such as error correction and data queries, necessitating considerable financial and time investment in their training or design. As DNA storage technologies, including sequencing and synthesis, continue to evolve rapidly, these codes may need to be retrained or redesigned to adapt to new constraints. In this study, we aim to design a method for adapting an existing DNA storage code to satisfy a new constraint, specifically concerning homopolymer variations. We present a simple and effective framework known as Transfer Coding, which directly maps DNA sequences from an original homopolymer constraint [Formula Omitted] to a new constraint [Formula Omitted]. This approach essentially combines the existing coding scheme with a Transfer encoder. The proposed method uses strategic base replacements to ensure compliance with constraints, achieving results close to the theoretical limit while keeping alterations to the original sequence minimal. Many DNA storage codes take into account homopolymer and GC-content constraints. Still, these codes often need to meet additional practical database requirements, such as error correction and data queries, necessitating considerable financial and time investment in their training or design. As DNA storage technologies, including sequencing and synthesis, continue to evolve rapidly, these codes may need to be retrained or redesigned to adapt to new constraints. In this study, we aim to design a method for adapting an existing DNA storage code to satisfy a new constraint, specifically concerning homopolymer variations. We present a simple and effective framework known as Transfer Coding, which directly maps DNA sequences from an original homopolymer constraint <tex-math notation="LaTeX">$h_{1}$ </tex-math> to a new constraint <tex-math notation="LaTeX">$h_{2}$ </tex-math>. This approach essentially combines the existing coding scheme with a Transfer encoder. The proposed method uses strategic base replacements to ensure compliance with constraints, achieving results close to the theoretical limit while keeping alterations to the original sequence minimal. |
| Author | Gao, Yunfei No, Albert |
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| Cites_doi | 10.1109/ALLERTON.2019.8919890 10.1093/nsr/nwaa007 10.1002/anie.201411378 10.1016/j.procs.2016.05.398 10.1073/pnas.2004821117 10.1109/LCOMM.2018.2866566 10.1109/LCOMM.2020.2991461 10.1038/nature11875 10.1109/ACCESS.2020.2980036 10.23919/JCN.2022.000008 10.1126/science.aaj2038 10.1093/bioinformatics/btab246 10.1038/s41467-021-24991-z 10.1126/science.1226355 10.1038/s41598-017-05188-1 10.1109/LCOMM.2019.2912572 |
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| SubjectTerms | Codes DNA storage DNA-to-DNA coding edit distance Error correction GC contents Gene sequencing homopolymer constraint |
| Title | Adaptable DNA Storage Coding: An Efficient Framework for Homopolymer Constraint Transitions |
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