laelbarlow / jackhmmerer

A snakemake workflow for iterative sequence profile searching using jackhmmer from the HMMer3 package.

JackHMMerer

This is a snakemake workflow for searching iteratively for similar sequences in amino acid sequence FASTA files using the jackhmmer program from the HMMer3 software package.

Overview

Installation

• Ensure you have Python3 and the Conda package and environment manager pre-installed on your system. Ideally, this should be run on a high-performance computing cluster.

• Clone the code repository from github to your computer by running the following shell command in your terminal:

  git clone https://github.com/laelbarlow/jackhmmerer.git
  

• Change directories into the cloned repository:

  cd jackhmmerer
  

• Install jackhmmerer (set up snakemake environment and profile for submitting jobs via your cluster's job scheduler), and run a test job.

  make install
  make dry_run
  

Procedure

• Put amino acid sequence FASTA files with sequences to be searched in the resources/FASTA_Databases directory.

• Assign each FASTA file to a taxonomic group (e.g., Eukaryotes, Archaea, or Bacteria) in a file resources/genome_ids_by_taxon.csv, wherein the first column is the taxonomic group name and the second column is a genome identifier (e.g., a EukProt ID).

• Put amino acid sequence FASTA files with sequences to be used as jackhmmer queries in the resources/FASTA_Queries directory. If any of these sequences contain more than one domain, they should be trimmed to include only the domain of interest.

• If necessary, customize the list of E-value thresholds (for the best domain in a sequence) to use for jackhmmer runs (the workflow will run the jackhmmer separately for each of the listed E-value thresholds).

  vim resources/evalue_thresholds.csv
  

• Run the workflow.

  make run
  

• View results. In particular:

  • The alignments in this directory may be of interest: results/convert_to_fasta. These are only the subsequences that matched the query sequence.
  • Also, full-length FASTA sequences for hits will be in this directory: results/retrieve_full_length_seqs.

License

MIT License

Copyright (c) 2021 Lael D. Barlow

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.