akshayayadav / hmmsearch-hmmscan-family-merging

Container for HMMSEARCH-HMMSCAN based family merging workflow

Tool for HMMSEARCH-HMMSCAN-based gene-family merging

This container contains the application for merging gene-families using a novel two-way HMMSEARCH-HMMSCAN search procedure. Each given family is searched against a combined database of all family sequences and the desired outgroup sequences, to find the candidate missing sequences for the family. The candidate missing sequences reverse searched against the combined database of family HMMs, and the sequences that find the original family as the best match are predicted missing sequences for the family. Finally, the predicted missing sequences from all the families are used to merge under-clustered families.

1. Downloading the container

docker pull akshayayadav/hmmsearch-hmmscan-family-merging

2. Preparing the data

Create a data directory <my_directory> with a user defined name. This directory MUST contain 3 items: family_fasta directory containing all the fasta files for the user-defined gene families, a family-outgroup-sequences.fa fasta file containing sequences from all the families and sequences from all the desired outgroups and a outgroups.list file listing the names of all the outgroup species (one per line) present in the family-outgroup-sequences.fa file. All the outgroup sequence headers in the family-outgroup-sequences.fa file MUST be prefixed with the respective outgroup species names present in outgroups.list file.

3. Running the analysis

Once the data is ready execute the workflow using the following command

docker run -v <absolute_path_to_the_data_directory>:/data akshayayadav/hmmsearch-hmmscan-family-merging run_analysis.sh