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 |
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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 |
Keywords
- R package
- gene prediction
- microbial genome annotation
- web application
ASJC Scopus subject areas
- Modelling and Simulation
- Molecular Biology
- Genetics
- Computational Mathematics
- Computational Theory and Mathematics