RIOT - Rapid Immunoglobulin Overview Tool - annotation of nucleotide and amino acid immunoglobulin sequences using an open germline database.

Dudzic, P.; Janusz, B.; Satlawa, T.; Chomicz, D.; Gawlowski, T.; Grabowski, R.; Jozwiak, P.; Tarkowski, M.; Mycielski, M.; Wrobel, S.; Krawczyk, K.

doi:10.1101/2024.08.12.607568

bioRxiv · 10.1101/2024.08.12.607568

RIOT - Rapid Immunoglobulin Overview Tool - annotation of nucleotide and amino acid immunoglobulin sequences using an open germline database.

Dudzic, P.·Janusz, B.·Satlawa, T.·Chomicz, D.·Gawlowski, T.·Grabowski, R.·Jozwiak, P.·Tarkowski, M.·Mycielski, M.·Wrobel, S.·Krawczyk, K.

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Abstract

Antibodies are a cornerstone of the immune system, playing a pivotal role in identifying and neutralizing infections caused by bacteria, viruses, and other pathogens. Understanding their structure, and function, can provide insights into both the bodys natural defenses and the principles behind many therapeutic interventions, including vaccines and antibody-based drugs. The analysis and annotation of antibody sequences, including the identification of variable, diversity, joining, and constant genes, as well as the delineation of framework regions and complementarity-determining regions, is essential for understanding their structure and function. Currently analyzing large volumes of antibody sequences is routine in antibody discovery, requiring fast and accurate tools. While there are existing tools designed for the annotation and numbering of antibody sequences, they often have limitations such as being restricted to either nucleotide or amino acid sequences, reliance on non-uniform germline databases, or slow execution times. Here we present Rapid Immunoglobulin Overview Tool (RIOT), a novel open-source solution for antibody numbering that addresses these shortcomings. RIOT handles nucleotide and amino acid sequence processing, comes with a free germline database, and is computationally efficient. We hope the tool will facilitate rapid annotation of antibody sequencing outputs for the benefit of understanding antibody biology and discovering novel therapeutics. AvailabilityRIOT is available at https://github.com/NaturalAntibody/riot_na.

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Dudzic, P., Janusz, B., Satlawa, T., Chomicz, D., Gawlowski, T., Grabowski, R., Jozwiak, P., Tarkowski, M., Mycielski, M., Wrobel, S., Krawczyk, K.. 2024-08-12. RIOT - Rapid Immunoglobulin Overview Tool - annotation of nucleotide and amino acid immunoglobulin sequences using an open germline database.. https://doi.org/10.1101/2024.08.12.607568

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