Generating Publication-Ready Prokaryotic Genome Annotations With DFAST

Methods Mol Biol. 2019;1962:215-226. doi: 10.1007/978-1-4939-9173-0_13.

Abstract

DDBJ Fast Annotation and Submission Tool (DFAST) is a genome annotation pipeline for prokaryotes, which also assists data submission to the public sequence database. It is available both as a web service and as a stand-alone tool that runs on local machines. DFAST can annotate a typical-sized bacterial genome within 5 min. The default annotation workflow contains a gene prediction phase for protein coding sequence, rRNA, tRNA, and CRISPR, and a functional annotation phase to infer protein functions. DFAST generates result files in standard annotation formats and data files for submission to DNA Data Bank of Japan (DDBJ). In this chapter, the annotation workflow and applications of DFAST are introduced.

Keywords: Annotation; Archaea; Bacteria; Database.

MeSH terms

  • Clustered Regularly Interspaced Short Palindromic Repeats
  • Data Display
  • Databases, Nucleic Acid*
  • Genome, Bacterial
  • Internet
  • Molecular Sequence Annotation / methods*
  • Prokaryotic Cells*
  • Proteins / genetics
  • Pseudogenes
  • Publishing
  • RNA, Ribosomal
  • RNA, Transfer
  • Software*
  • Workflow

Substances

  • Proteins
  • RNA, Ribosomal
  • RNA, Transfer