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bioRxiv · 10.1101/2025.04.26.650794

OrfViralScan 3.0: An intuitive tool for the identification and tracking of open reading frames in viral genomes

Reinosa, R.
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Abstract

The identification and analysis of open reading frames (ORFs) are fundamental steps in genome annotation, which requires accurate bioinformatics tools. OrfViralScan 3.0 is presented, a desktop application developed in Java (requires Java 11 to run), featuring an intuitive graphical user interface (GUI) designed to facilitate the annotation and tracking of ORFs. The program offers functionalities to search for ORFs (initiated by ATG) in individual sequences (ORF Search), track specific ORFs based on length and location across multiple genomes or sequence sets (Track Specific ORF), preprocess FASTA files to standardize formatting (Preprocess File), and split large genomes into manageable fragments (Divide Into Fragments). The utility of OrfViralScan 3.0 is demonstrated through the analysis of the SARS-CoV-2 reference genome (NC_045512.2), the successful tracking of the Spike protein in 983 out of 1000 complete viral genomes, and the preparation of the Escherichia coli genome (NC_000913.3) for fragmented analysis. The softwares capabilities, limitations, and potential future applications are discussed. An example is also included featuring the SARS-CoV-2 Spike protein, showing the folded ORF obtained with OrfViralScan 3.0 using AlphaFold 3. The programs source code is available on GitHub under the GNU GPLv3 license. Contactroberto117343@gmail.com

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Reinosa, R.. 2025-04-28. OrfViralScan 3.0: An intuitive tool for the identification and tracking of open reading frames in viral genomes. https://doi.org/10.1101/2025.04.26.650794

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