Prokaryotic Contig Annotation Pipeline Server: Web Application for a Prokaryotic Genome Annotation Pipeline Based on the Shiny App Package
- Authors
- Park, Byeonghyeok; Baek, Min-Jeong; Min, Byoungnam; Choi, In-Geol
- Issue Date
- 9월-2017
- Publisher
- MARY ANN LIEBERT, INC
- Keywords
- gene prediction; microbial genome annotation; R package; web application
- Citation
- JOURNAL OF COMPUTATIONAL BIOLOGY, v.24, no.9, pp.917 - 922
- Indexed
- SCIE
SCOPUS
- Journal Title
- JOURNAL OF COMPUTATIONAL BIOLOGY
- Volume
- 24
- Number
- 9
- Start Page
- 917
- End Page
- 922
- URI
- https://scholar.korea.ac.kr/handle/2021.sw.korea/82380
- DOI
- 10.1089/cmb.2017.0066
- ISSN
- 1066-5277
- Abstract
- Genome annotation is a primary step in genomic research. To establish a light and portable prokaryotic genome annotation pipeline for use in individual laboratories, we developed a Shiny app package designated as "P-CAPS'' (Prokaryotic Contig Annotation Pipeline Server). The package is composed of R and Python scripts that integrate publicly available annotation programs into a server application. P-CAPS is not only a browser-based interactive application but also a distributable Shiny app package that can be installed on any personal computer. The final annotation is provided in various standard formats and is summarized in an R markdown document. Annotation can be visualized and examined with a public genome browser. A benchmark test showed that the annotation quality and completeness of P-CAPS were reliable and compatible with those of currently available public pipelines.
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Collections - Graduate School > Department of Biotechnology > 1. Journal Articles
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