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bioRxiv · 10.1101/2024.02.28.582384

SEGUID v2: Extending SEGUID checksums for circular, linear, single- and double-stranded biological sequences

Pereira, H.·Silva, P. C.·Davis, W. M.·Abraham, L.·Babnigg, G.·Bengtsson, H.·Johansson, B.
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Abstract

BackgroundSynthetic biology involves combining different DNA fragments, each containing functional biological parts, to address specific problems. Fundamental gene-function research often requires cloning and propagating DNA fragments, such as those from the iGEM Parts Registry or Addgene, typically distributed as circular plasmids. Addgenes repository alone offers around 150,000 plasmids. To ensure data integrity, cryptographic checksums can be calculated for the sequences. Each sequence has a unique checksum, making checksums useful for validation and quick lookups of associated annotations. For example, the SEGUID checksum uniquely identifies protein sequences with a 27-character string. ObjectivesThe original SEGUID, while effective for protein sequences and single-stranded DNA (ssDNA), is not suitable for circular DNA since there is no natural starting position nor for double-stranded DNA (dsDNA) since two separate sequences are present. Challenges include how to uniquely represent linear dsDNA, circular ssDNA, and circular dsDNA. To meet these needs, we propose SEGUID v2, which extends the original SEGUID to handle additional types of sequences. ConclusionsSEGUID v2 produces orientation and rotation in-variant checksums for single-stranded, double-stranded, possibly staggered, linear, and circular DNA and RNA sequences. Customizable alphabets allow for other types of sequences. In contrast to the original SEGUID, which uses Base64, SEGUID v2 uses Base64url to encode the SHA-1 hash. This ensures SEGUID v2 checksums can be used as-is in filenames, regardless of platform, and in URLs, with minimal friction. AvailabilitySEGUID v2 is readily available for major program-ming languages, distributed under the MIT license. JavaScript package seguid is available on npm, Python package seguid on PyPi, R package seguid on CRAN, and a Tcl script on GitHub. These tools, along with documentation, examples, and an online SEGUID Calculator, can be found at https://www.seguid.org.

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Pereira, H., Silva, P. C., Davis, W. M., Abraham, L., Babnigg, G., Bengtsson, H., Johansson, B.. 2024-03-03. SEGUID v2: Extending SEGUID checksums for circular, linear, single- and double-stranded biological sequences. https://doi.org/10.1101/2024.02.28.582384

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