使用DFAST生成可用于发表的原核生物基因组注释。

Generating Publication-Ready Prokaryotic Genome Annotations with DFAST.

作者信息

Tanizawa Yasuhiro, Fujisawa Takatomo, Arita Masanori, Nakamura Yasukazu

机构信息

Department of Informatics, National Institute of Genetics, Shizuoka, Japan.

RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan.

出版信息

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

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

PMID:31020563

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.

摘要

DDBJ快速注释与提交工具（DFAST）是一种用于原核生物的基因组注释流程，它还协助向公共序列数据库提交数据。它既可以作为网络服务使用，也可以作为在本地机器上运行的独立工具使用。DFAST可以在5分钟内注释一个典型大小的细菌基因组。默认的注释工作流程包括一个针对蛋白质编码序列、rRNA、tRNA和CRISPR的基因预测阶段，以及一个推断蛋白质功能的功能注释阶段。DFAST以标准注释格式生成结果文件，并生成用于提交给日本DNA数据库（DDBJ）的数据文件。在本章中，将介绍DFAST的注释工作流程和应用。