P2T2: Protein Panoramic annoTation Tool for the interpretation of protein coding genetic variants

Elias Devoe, Gavin R. Oliver, Roman Zenka, Patrick R. Blackburn, Margot A. Cousin, Nicole J. Boczek, Jean Pierre A. Kocher, Raul Alfredo Urrutia, Eric W. Klee, Michael T. Zimmermann

Research output: Contribution to journalArticlepeer-review

Abstract

Motivation: Genomic data are prevalent, leading to frequent encounters with uninterpreted variants or mutations with unknown mechanisms of effect. Researchers must manually aggregate data from multiple sources and across related proteins, mentally translating effects between the genome and proteome, to attempt to understand mechanisms. Materials and methods: P2T2 presents diverse data and annotation types in a unified protein-centric view, facilitating the interpretation of coding variants and hypothesis generation. Information from primary sequence, domain, motif, and structural levels are presented and also organized into the first Paralog Annotation Analysis across the human proteome. Results: Our tool assists research efforts to interpret genomic variation by aggregating diverse, relevant, and proteome-wide information into a unified interactive web-based interface. Additionally, we provide a REST API enabling automated data queries, or repurposing data for other studies. Conclusion: The unified protein-centric interface presented in P2T2 will help researchers interpret novel variants identified through next-generation sequencing. Code and server link available at github.com/GenomicInterpretation/p2t2.

Original languageEnglish (US)
Article numberooab065
JournalJAMIA Open
Volume4
Issue number3
DOIs
StatePublished - Jul 1 2021

Keywords

  • data aggregation
  • genetic variation
  • high-throughput nucleotide sequencing
  • molecular sequence annotation
  • protein annotations

ASJC Scopus subject areas

  • Health Informatics

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