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.
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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
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Change directories into the cloned repository:
cd jackhmmerer
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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
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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
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Run the workflow.
make run
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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
.
- The alignments in this directory may be of interest:
MIT License
Copyright (c) 2021 Lael D. Barlow
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