Bioinformatics web tools and servers are a powerful way for researchers to share valuable computational tools. They are ideal because users can run analyses in their browsers without having to download, set up, and run code on their local system. However, bioinformatics tool development requires web development proficiency and server costs which can be a barrier to entry. Google Colaboratory (Colab) is an online interactive code environment available to anyone with a free account. Colab is easy for both the developer and user. It allows researchers to make code available without needing web development skills. Users can customize code easily through Colab, which is beneficial since current bioinformatics web tools do not allow the user to edit code and perform customized operations. Also, Colab allows for easy collaboration and editing of code without concerns about platform compatibility between computers. Due to its user-friendly and customizable properties, we propose using Colab for developing bioinformatics tools. In this case study, we demonstrate implementation of the OKtool on Colab, a Python-based tool for calculating overlapping k-mers of desired length from a list of protein or DNA sequences. Applications include motif analysis and antigenic epitope analysis. It is a highly-customizable tool fully implemented in Colab that provides a FASTA file of k-mers derived from any given list of sequences. Overall, our work demonstrates the potential for bioinformatics tool development on Colab. OKtool is freely accessible at oktool.cloud.
Short link: oktool.cloud
Github link: https://github.com/andrewgcodes/OKtool
Simply open the Google Colab link to run the code. Step by step instructions are provided. No downloads are necessary. If unable to access Colab, download the Github IPYNB file and open in Jupyter on your system. The only needed library is Pandas, which can be installed via pip.