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

Author:

Gonçalves Rafael,Santos AndersonORCID

Abstract

AbstractGenome 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 athttps://github.com/santosardr/medpipe-ms.git.

Publisher

Cold Spring Harbor Laboratory

同舟云学术

1.学者识别学者识别

2.学术分析学术分析

3.人才评估人才评估

"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370

www.globalauthorid.com

TOP

Copyright © 2019-2024 北京同舟云网络信息技术有限公司
京公网安备11010802033243号  京ICP备18003416号-3