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DFAST and DAGA: web-based integrated genome annotation tools and resources.

Yasuhiro Tanizawa1, Takatomo Fujisawa2, Eli Kaminuma2

  • 1Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan; Center for Information Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan.

Bioscience of Microbiota, Food and Health
|November 22, 2016
PubMed
Summary

The DDBJ Fast Annotation and Submission Tool (DFAST) and its associated genome repository (DAGA) improve the quality and taxonomic accuracy of lactic acid bacteria genome data. These tools aid researchers in submitting reliable genomic information and discovering new intraspecific variations.

Keywords:
LactobacillusPediococcusannotationdatabasegenomelactic acid bacteria

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Ensuring data quality and correct taxonomic identification in public sequence databases is a persistent challenge.
  • Existing bioinformatics tools may require specialized skills, limiting accessibility for some researchers.

Purpose of the Study:

  • To develop and present a comprehensive genome annotation pipeline (DFAST) with integrated quality and taxonomy assessment tools.
  • To establish a curated genome repository (DAGA) for lactic acid bacteria, enhancing data accessibility and reusability.
  • To identify and correct misidentified genomes in public databases, improving the reliability of available genomic resources.

Main Methods:

  • Development of the DDBJ Fast Annotation and Submission Tool (DFAST) for seamless online genome annotation and submission.
  • Construction of curated reference protein databases for lactic acid bacteria.
  • Creation of the DFAST Archive of Genome Annotation (DAGA), a repository of 1,421 annotated genomes.
  • Utilizing average nucleotide identity (ANI) for accurate taxonomic assessment and species delineation.
  • Analysis of DAGA data to identify intraspecific subgroups within bacterial species.

Main Results:

  • DFAST provides quality and taxonomy assessment tools, enabling ready-to-submit genome annotations.
  • DAGA houses 1,421 consistently annotated genomes of *Lactobacillus* and *Pediococcus* species.
  • Correction of mislabeled or misidentified genomes in public databases has been performed.
  • Discovery of significant intraspecific subgroups in *Lactobacillus gasseri* and *Lactobacillus jensenii* based on ANI analysis.

Conclusions:

  • DFAST and DAGA offer a robust solution for high-quality genome annotation and data management in lactic acid bacteria.
  • The developed tools and repository facilitate bioinformatics-naive users and improve the overall quality of public genomic data.
  • The findings highlight the utility of DAGA in uncovering novel microbial diversity and refining taxonomic classifications.