pLannotate is web server for automatically annotating engineered plasmids.
Please visit http://plannotate.barricklab.org/
If you wish you to use pLannotate as a local server or to use as a command line tool, please follow the instructions below (requires Conda).
Download the compressed source code as well as the compressed BLAST (and associated) databases from the releases page. Uncompress the source code, though leave the BLAST databases compressed for now. Move the files to a directory of your choice.
On the command line, navigate to the directory where you have placed the pLannotate folder and compressed databases.
Enter the following commands:
tar -zxf BLAST_dbs.tar.gz -C ./pLannotate*/plannotate/data && rm BLAST_dbs.tar.gz
cd pLannotate*
conda env create -f environment.yml
conda activate plannotate
python setup.py install
To launch pLannotate as a local web server:
plannotate streamlit
After execution of the final command, pLannotate should launch in your default web browser, or you may simply navigate to http://localhost:8501 in your web browser.
To annotate FASTA or GenBank files and generate the interactive plasmid maps on the command line, follow the above instructions to install pLannotate.
We can check the options using the following command:
plannotate batch --help
Usage: plannotate batch [OPTIONS]
Annotates engineered DNA sequences, primarily plasmids. Accepts a FASTA file
and outputs a gbk file with annotations, as well as an optional interactive
plasmid map as an HTLM file.
Options:
-i, --input TEXT location of a FASTA or GBK file; < 50,000 bases
-o, --output TEXT location of output folder. DEFAULT: current dir
-f, --file_name TEXT name of output file (do not add extension). DEFAULT:
input file name
-s, --suffix TEXT suffix appended to output files. Use '' for no suffix.
DEFAULT: '_pLann'
-y, --yaml_file TEXT path to YAML file for custom databases. DEFAULT:
builtin
-l, --linear enables linear DNA annotation
-h, --html creates an html plasmid map in specified path
-c, --csv creates a cvs file in specified path
-d, --detailed uses modified algorithm for a more-detailed search
with more false positives
-x, --no_gbk supresses GenBank output file
--help Show this message and exit.
Example usage:
plannotate batch -i ./plannotate/data/fastas/pUC19.fa --html --output ~/Desktop/ --file_name pLasmid
Custom databases can be added by supplying pLannotate a custom YAML file. To create the default YAML file, enter the following command:
plannotate yaml > plannotate_default.yaml
This configuration file can be edited to point to other external databases that you wish to use. When launching pLannotate, you can specify the path to your custom YAML file using the --yaml_file option.
pLannotate is currently developed by Matt McGuffie at the Barrick lab, University of Texas at Austin, Austin, Texas.