Mutually uncorrelated primers for DNA-based data storage
We introduce the notion of weakly mutually uncorrelated (WMU) sequences, motivated by applications in DNA-based data storage systems and synchronization between communication devices. WMU sequences are characterized by the property that no sufficiently long suffix of one sequence is the prefix of th...
| Main Authors: | , , , |
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| Other Authors: | |
| Format: | Journal Article |
| Language: | English |
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2020
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| Online Access: | https://hdl.handle.net/10356/145347 |
| _version_ | 1826124430473953280 |
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| author | Tabatabaei Yazdi, S. M. H. Kiah, Han Mao Gabrys, Ryan Milenkovic, Olgica |
| author2 | School of Physical and Mathematical Sciences |
| author_facet | School of Physical and Mathematical Sciences Tabatabaei Yazdi, S. M. H. Kiah, Han Mao Gabrys, Ryan Milenkovic, Olgica |
| author_sort | Tabatabaei Yazdi, S. M. H. |
| collection | NTU |
| description | We introduce the notion of weakly mutually uncorrelated (WMU) sequences, motivated by applications in DNA-based data storage systems and synchronization between communication devices. WMU sequences are characterized by the property that no sufficiently long suffix of one sequence is the prefix of the same or another sequence. WMU sequences used for primer design in DNA-based data storage systems are also required to be at large mutual Hamming distance from each other, have balanced compositions of symbols, and avoid primer-dimer byproducts. We derive bounds on the size of WMU and various constrained WMU codes and present a number of constructions for balanced, error-correcting, primer-dimer free WMU codes using Dyck paths, prefix-synchronized, and cyclic codes. |
| first_indexed | 2024-10-01T06:20:30Z |
| format | Journal Article |
| id | ntu-10356/145347 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T06:20:30Z |
| publishDate | 2020 |
| record_format | dspace |
| spelling | ntu-10356/1453472020-12-17T09:25:25Z Mutually uncorrelated primers for DNA-based data storage Tabatabaei Yazdi, S. M. H. Kiah, Han Mao Gabrys, Ryan Milenkovic, Olgica School of Physical and Mathematical Sciences Engineering::Computer science and engineering Biocomputing Biological Information Theory We introduce the notion of weakly mutually uncorrelated (WMU) sequences, motivated by applications in DNA-based data storage systems and synchronization between communication devices. WMU sequences are characterized by the property that no sufficiently long suffix of one sequence is the prefix of the same or another sequence. WMU sequences used for primer design in DNA-based data storage systems are also required to be at large mutual Hamming distance from each other, have balanced compositions of symbols, and avoid primer-dimer byproducts. We derive bounds on the size of WMU and various constrained WMU codes and present a number of constructions for balanced, error-correcting, primer-dimer free WMU codes using Dyck paths, prefix-synchronized, and cyclic codes. 2020-12-17T09:25:25Z 2020-12-17T09:25:25Z 2018 Journal Article Tabatabaei Yazdi, S. M. H., Kiah, H. M., Gabrys, R., & Milenkovic, O. (2018). Mutually uncorrelated primers for DNA-based data storage. IEEE Transactions on Information Theory, 64(9), 6283-6296. doi:10.1109/TIT.2018.2792488 1557-9654 https://hdl.handle.net/10356/145347 10.1109/TIT.2018.2792488 9 64 6283 6296 en IEEE Transactions on Information Theory © 2018 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works. The published version is available at: https://doi.org/10.1109/TIT.2018.2792488 |
| spellingShingle | Engineering::Computer science and engineering Biocomputing Biological Information Theory Tabatabaei Yazdi, S. M. H. Kiah, Han Mao Gabrys, Ryan Milenkovic, Olgica Mutually uncorrelated primers for DNA-based data storage |
| title | Mutually uncorrelated primers for DNA-based data storage |
| title_full | Mutually uncorrelated primers for DNA-based data storage |
| title_fullStr | Mutually uncorrelated primers for DNA-based data storage |
| title_full_unstemmed | Mutually uncorrelated primers for DNA-based data storage |
| title_short | Mutually uncorrelated primers for DNA-based data storage |
| title_sort | mutually uncorrelated primers for dna based data storage |
| topic | Engineering::Computer science and engineering Biocomputing Biological Information Theory |
| url | https://hdl.handle.net/10356/145347 |
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