Generating Publication-Ready Prokaryotic Genome Annotations with DFAST

Yasuhiro Tanizawa; Takatomo Fujisawa; Masanori Arita; Yasukazu Nakamura

doi:10.1007/978-1-4939-9173-0_13

Generating Publication-Ready Prokaryotic Genome Annotations with DFAST

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

Authors

Yasuhiro Tanizawa¹, Takatomo Fujisawa², Masanori Arita^{2

3}, Yasukazu Nakamura²

Affiliations

¹ Department of Informatics, National Institute of Genetics, Shizuoka, Japan. ytanizaw@nig.ac.jp.
² Department of Informatics, National Institute of Genetics, Shizuoka, Japan.
³ RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan.

PMID: 31020563
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