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'Democratized' genomic enzymology web tools for functional assignment.

Rémi Zallot1, Nils O Oberg1, John A Gerlt2

  • 1Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, United States.

Current Opinion in Chemical Biology
|October 1, 2018
PubMed
Summary

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Genomic dark matter, or uncharacterized proteins, requires accessible web tools for functional discovery. This review highlights tools and data capture methods to improve enzyme annotation and understand novel protein functions.

Area of Science:

  • Bioinformatics
  • Genomics
  • Enzymology

Background:

  • Exponential growth in protein sequence data from reduced sequencing costs creates vast genomic dark matter.
  • The rate of data generation outpaces functional characterization, necessitating new approaches for discovery.

Purpose of the Study:

  • To review the utility of web tools for functional assignment of novel enzymes and proteins.
  • To describe methods for capturing published functional data to enhance annotation quality.

Main Methods:

  • Discussion of publicly accessible genomic enzymology web tools.
  • Exploration of mechanisms for integrating published functional data into databases.

Main Results:

  • Web tools are crucial for leveraging protein and genome databases for functional discovery.

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  • Improved data capture can enhance both curated and automated annotation transfer.

    • Conclusions:

    • Democratized web tools are essential for exploring genomic dark matter.
    • A robust data capture mechanism is needed to improve the accuracy and transferability of functional annotations.