This is a fast tool for preliminary gene analysis which offers an interface for visualising descriptive metrics about the genes
This is the deployed version
This is the link to the repo
In order to run the app locally, you will need to have conda installed.
Once the directory is been downloaded or cloned locally, you will need to create a conda environment:
conda env create -f environment.yml
You can check for the successful creation of the environment using:
conda spyder_app list
Once the environment is created, using the terminal:
- Move into the directory
cd biospyder_app - Activate the conda environment
conda activate spyder_app - Run the app
python app.py
The local host server will run on port 8000
Once the server is running, or the heroku server has responded, you will find yourself on the landing page, where you can upload a .fasta or .csv file containing genomic sequences.
After uploading a file in the correct format, you will be prompted with the number of sequences loaded, as well as a dropdown menu indicating to select one of the sequences for further details.
Once one of the sequences is chosen, the app will present you with metrics about the selected sequence, including length, base distribution and 10bp sequence with highest GC content.
The app is based on Dash, but implements the use of pandas for data handling, pytest for testing and gunicorn for deploying.
Future features include:
- Blasting the sequence against the NCBI database
- Local alignment of sequences
- Sequence translation and inference of 3D structure
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