Pannotator integrated with Medpipe provides immunological and subcellular location features using a microservice

Abstract

Genome sequencing and assembly are trivial tasks nowadays. After assembling contigs and scaffolds from a genome, the subsequent step is annotation. An annotation evidencing the expected features, like rRNA, tRNA, and CDS, is a signal of the quality of our sequencing and assembly. Different techniques to obtain and reproduce DNA samples, as well as sequencing and assembly of genomes, can impact the quality of a genome's expected features. The Pannotator tool was conceived as an aid annotation tool focusing on the differences between assembling and its reference genome. Some of the key features for bacterial genome annotations are the subcellular location and immunological potential of a CDS. Instead of reimplementing the prediction of these features in Pannotator, we leveraged the capabilities of our microservice to provide them. In the end, Medpipe software was not modified, and Pannotator underwent minor changes to incorporate the subcellular location and immunological potential of all exported proteins annotated by the tool. Moreover, our Medpipe microservice can also be incorporated into other software. The Medpipe microservice is open to anyone, not only to our Pannotator tool. The successful integration of Medpipe to Pannotator, powered by the Medpipe microservice, offers a powerful approach to advanced genomic analysis. The Medpipe microservice, built on Kotlin with the Spring Boot framework, is instrumental in the automation of Medpipe processing. It achieves this using REST endpoints, such as the execution of Medpipe in an asynchronous manner, status retrieval, and prediction generation, which enhance the modularity and scalability of the microservice. The availability of endpoint documentation, detailed request examples, and logs make our microservice user-friendly. The results of this integration demonstrate the value of the information provided by Medpipe, enriching genomic annotation with additional details, such as the density of mature epitopes (MED) and protein subcellular location classification. The Pannotator has evolved beyond basic function annotation and now provides data on immunological potential, structure, and subcellular location after being integrated with our microservice. The Medpipe microservice is available at https://github.com/santosardr/medpipe-ms.git.