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.
| Original language | English |
|---|---|
| Pages (from-to) | 917-922 |
| Number of pages | 6 |
| Journal | Journal of Computational Biology |
| Volume | 24 |
| Issue number | 9 |
| DOIs | |
| Publication status | Published - 2017 Sep 1 |
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Keywords
- gene prediction
- microbial genome annotation
- R package
- web application
ASJC Scopus subject areas
- Modelling and Simulation
- Molecular Biology
- Genetics
- Computational Theory and Mathematics
- Computational Mathematics
Cite this
Prokaryotic contig annotation pipeline server : Web application for a prokaryotic genome annotation pipeline based on the shiny app package. / Park, Byeonghyeok; Baek, Min Jeong; Min, Byoungnam; Choi, In-Geol.
In: Journal of Computational Biology, Vol. 24, No. 9, 01.09.2017, p. 917-922.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Prokaryotic contig annotation pipeline server
T2 - Web application for a prokaryotic genome annotation pipeline based on the shiny app package
AU - Park, Byeonghyeok
AU - Baek, Min Jeong
AU - Min, Byoungnam
AU - Choi, In-Geol
PY - 2017/9/1
Y1 - 2017/9/1
N2 - 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.
AB - 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.
KW - gene prediction
KW - microbial genome annotation
KW - R package
KW - web application
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UR - http://www.scopus.com/inward/citedby.url?scp=85029381396&partnerID=8YFLogxK
U2 - 10.1089/cmb.2017.0066
DO - 10.1089/cmb.2017.0066
M3 - Article
C2 - 28632399
AN - SCOPUS:85029381396
VL - 24
SP - 917
EP - 922
JO - Journal of Computational Biology
JF - Journal of Computational Biology
SN - 1066-5277
IS - 9
ER -