Tool for protein-domain-composition-based-gene-family scoring

This container contains application for scoring gene-families using their Pfam protein domain composition. Cosine function is used to compare the protein domains of the sequences within gene-families.

1. Downloading the container

docker pull akshayayadav/genefamily-domain-composition-cosine-scoring

2. Preparing the data

Create a data directory <my_directory> with a user-defined name. This directory MUST contain a directory called family_fasta containing fasta files for the desired gene families and directory named pfam_database containing the Pfam database HMM file. The HMM file must be hmmpressed using the hmmpress tool from the HMMER package.

3. Running the analysis

Execute the analysis on the prepared data with n cores using the following command

docker run -v <absolute_path_to_the_data_directory>:/data akshayayadav/genefamily-domain-composition-cosine-scoring run_analysis.sh -c <n>