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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| Format: | Article |
| Language: | English |
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IEEE
2024-01-01
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| Series: | IEEE Access |
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| Online Access: | https://ieeexplore.ieee.org/document/10398196/ |
| _version_ | 1797348717707132928 |
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| author | Yunfei Gao Albert No |
| author_facet | Yunfei Gao Albert No |
| author_sort | Yunfei Gao |
| collection | DOAJ |
| description | 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 <inline-formula> <tex-math notation="LaTeX">$h_{1}$ </tex-math></inline-formula> to a new constraint <inline-formula> <tex-math notation="LaTeX">$h_{2}$ </tex-math></inline-formula>. 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. |
| first_indexed | 2024-03-08T12:10:00Z |
| format | Article |
| id | doaj.art-c4d44ad6ecb148e2beff60a9da79e426 |
| institution | Directory Open Access Journal |
| issn | 2169-3536 |
| language | English |
| last_indexed | 2024-03-08T12:10:00Z |
| publishDate | 2024-01-01 |
| publisher | IEEE |
| record_format | Article |
| series | IEEE Access |
| spelling | doaj.art-c4d44ad6ecb148e2beff60a9da79e4262024-01-23T00:04:18ZengIEEEIEEE Access2169-35362024-01-01129976998310.1109/ACCESS.2024.335330510398196Adaptable DNA Storage Coding: An Efficient Framework for Homopolymer Constraint TransitionsYunfei Gao0https://orcid.org/0000-0003-0543-2091Albert No1https://orcid.org/0000-0002-6346-4182Department of Electronic and Electrical Engineering, Hongik University, Seoul, South KoreaDepartment of Electronic and Electrical Engineering, Hongik University, Seoul, South KoreaMany 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 <inline-formula> <tex-math notation="LaTeX">$h_{1}$ </tex-math></inline-formula> to a new constraint <inline-formula> <tex-math notation="LaTeX">$h_{2}$ </tex-math></inline-formula>. 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.https://ieeexplore.ieee.org/document/10398196/DNA storageDNA-to-DNA codingedit distanceGC contentshomopolymer constraint |
| spellingShingle | Yunfei Gao Albert No Adaptable DNA Storage Coding: An Efficient Framework for Homopolymer Constraint Transitions IEEE Access DNA storage DNA-to-DNA coding edit distance GC contents homopolymer constraint |
| title | Adaptable DNA Storage Coding: An Efficient Framework for Homopolymer Constraint Transitions |
| title_full | Adaptable DNA Storage Coding: An Efficient Framework for Homopolymer Constraint Transitions |
| title_fullStr | Adaptable DNA Storage Coding: An Efficient Framework for Homopolymer Constraint Transitions |
| title_full_unstemmed | Adaptable DNA Storage Coding: An Efficient Framework for Homopolymer Constraint Transitions |
| title_short | Adaptable DNA Storage Coding: An Efficient Framework for Homopolymer Constraint Transitions |
| title_sort | adaptable dna storage coding an efficient framework for homopolymer constraint transitions |
| topic | DNA storage DNA-to-DNA coding edit distance GC contents homopolymer constraint |
| url | https://ieeexplore.ieee.org/document/10398196/ |
| work_keys_str_mv | AT yunfeigao adaptablednastoragecodinganefficientframeworkforhomopolymerconstrainttransitions AT albertno adaptablednastoragecodinganefficientframeworkforhomopolymerconstrainttransitions |