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

Area of Science:

• Synthetic biology
• Bioinformatics
• Molecular biology

Background:

• Synthetic biology relies on combining DNA fragments for research.
• DNA sequences are often distributed as plasmids, necessitating data integrity checks.
• Cryptographic checksums like SEGUID aid in validating sequences and annotations.

Purpose of the Study:

• To extend the SEGUID checksum to handle various DNA and RNA sequence types.
• To address limitations of the original SEGUID for circular and double-stranded nucleic acids.
• To develop a robust method for unique sequence identification.

Main Methods:

• Developed SEGUID v2, an extension of the original SEGUID algorithm.
• Implemented orientation and rotation invariance for diverse sequence structures.
• Utilized Base64url encoding of SHA-1 hashes for improved compatibility.

Main Results:

• SEGUID v2 generates unique checksums for linear, circular, single-stranded, and double-stranded DNA/RNA.
• Checksums are compatible with filenames and URLs due to Base64url encoding.
• The method supports customizable alphabets for various sequence types.

Conclusions:

• SEGUID v2 provides a universal solution for sequence checksums, enhancing data integrity.
• The new method overcomes limitations of previous approaches for complex nucleic acid structures.
• SEGUID v2 is accessible across major programming languages and platforms.