Methods for analyzing next-generation sequencing data IX.Genome annotation, visualization, and registration to DDBJ

Abstract

Genome annotation is a fundamental process in the sequence analysis, through which biological knowledge is generated from sequenced genomic data. Good annotation not only enhances our own downstream analyses but also promotes subsequent researches by others because it can propagate through public sequence databases. In this article, we will show how annotated genomic data are described in the public databases. And then, we will introduce how to use the bacterial annotation pipeline DFAST (DDBJ Fast Annotation and Submission Tool). DFAST is developed to facilitate quick and accurate genome annotation as well as data submission to DDBJ. It was originally designed specific for lactic acid bacteria and now extended to other organism groups. We finally present a method to visualize chromosome maps from DFAST annotation results. Supplementary materials are available at our web site, http://www.iu.a.u-tokyo.ac.jp/~
kadota/r_seq.html#about_book_JSLAB.