Shiny application for annotating and plotting short gene segments with Prokka, BLAST and genoPlotR. The application is designed for comparison of short gene segments (rather than whole genomes) such as mobile genetic elements, viruses or other interesting genome fragments from prokaryotic organisms.
Alpha Version: several options in the interface are not wired up, error checks are not properly implemented, plot downloads are not implemented; please use with patience.
shiny::runGitHub('shinyGenes', 'esteinig')
Files
- Single GenBank format from NCBI. This allows for the download of gene segments from GenBank. Files are converted to FASTA for comparison with BLASTN.
- Single FASTA format when annotating with Prokka. This allows for the input of unannotated gene fragments, which are piped and annotated locally with Prokka. Requires a local installation of Prokka.
Note
- All file names need to be ordered by the desired final placement of segments in the plot - this can best be achieved by numbering the files in the desired order
- When annotating with Prokka, contig names in the FASTA files must be less than 20 character
- Two or more files must be loaded for plotting with shinyGenes
Examples
1_SCCmec_IV_M03-68.gbk,2_SCCmec_IV_CM11.gbk,...1_SCCmec_IV_M03-68.fasta,2_SCCmec_IV_CM11.fasta,...
R version > 3.2
Install packages manually or use install.R from within R:
source(install.R)
Packages:
- shiny
- shinydashboard
- shinyjs
- seqinr
- DT
- genoPlotR
BLAST:
Very simple to set up on Ubuntu, head over to NCBI to check the process for Windows OS.
sudo apt-get install ncbi-blast+
Prokka (optional):
Victorian Bioinformatics Consortium
Note that if you would like to use the annotation with Prokka, this is only possible on Linux and Mac OS X. For more information and installation guidelines, head over to Torsten Seemann's excellent GitHub.
Prokka is very easy to set up, for Ubuntu the only dependency that needed to be installed was BioPerl:
sudo apt-get install bioperl
It seems like there is a clash between RStudio and the system function ability to find programs placed in the user PATH. If you want to use Prokka, please run the application directly from R in the Terminal.
This is a simple tutorial to operate the user interface of shinyGenes. A more detailed manual is in preperation and will be included in the release version.
Step 1: Load example files (GenBank) in Settings and Pipeline.
Step 2: Check the annotation box in Plot
Step 3: Press Run in Pipeline
Step 4: Switch to Data. You can change the names and colours of the segments here and select additional options for the plot in Settings and Plot
Step 5: Switch to Plot and look at those shiny Genes!
...
...
Prokka:
Seemann T. (2014), Prokka: rapid prokaryotic genome annotation, Bioinformatics, 30(14):2068-9. PMID:24642063
genoPlotR:
Lionel G., Kultima, J.R. and Andersson, S.E.G (2010): genoPlotR: comparative gene and genome visualization in R. Bioinformatics, 26(18):2334-2335
Please give some love to the brilliant people behind the packages used in this applications, including: