Using selenoprofiles in Docker

Pull the image

The Docker image of Selenoprofiles provides a complete, ready-to-use environment with all optional dependencies already installed. This is the recommended way to run Selenoprofiles if you want to avoid managing dependencies:

The official Docker image is available on Docker Hub:
docker pull maxtico/selenoprofiles_container:latest

Run Selenoprofiles in Docker

You can run Selenoprofiles directly within the container. In most cases, you’ll want to mount your working directory so results and input files can be accessed outside of the container. Here’s a complete example command:

docker run --rm -v $(pwd):/mnt maxtico/selenoprofiles_container:latest \
  selenoprofiles \
  -o /mnt/{selenoprofiles_output_folder} \
  -t /mnt/{species_genome} \
  -s {species} \
  -p {profile} \
  -temp /mnt/{temp_folder}

Let’s go step by step with a simple example.

Searching for selenoproteins in the human genome

Let’s imagine we are working with the human genome and we want to check for the presence of SELENOP and SELENOS using Selenoprofiles. First, make sure your genome file (e.g. genome.fa) is in your current working directory. Then, run the following command:

docker run --rm -v $(pwd):/mnt maxtico/selenoprofiles_container:latest \
    selenoprofiles \
    -o /mnt/selenoprofiles_out \
    -t /mnt/genome.fa \
    -s Homo_sapiens \
    -p GPX,DIO \
    -temp /mnt/temp
    -output_gtf_file /mnt/homo_sapiens.gtf

The Docker image also includes all Selenoprofiles utilities, which can be run in the same way.

Collecting results from runs on multiple targets

When running Selenoprofiles on several target genomes (for example, across different species), each run produces one or more .ali files — one for every profile where at least one hit was found. To combine the results from different runs into a single set of alignments, you can use the built-in join utility.

For example, suppose you have already run Selenoprofiles on several genomes and stored all outputs under selenoprofiles_out. You can merge the alignments for specific profiles (e.g. GPX and DIO) as follows:

docker run --rm -v $(pwd):/mnt maxtico/selenoprofiles_container:latest \
    selenoprofiles \
    join \
    -d /mnt/selenoprofiles_out \
    -p GPX,DIO \
    -o /mnt/join_results

Classifying predictions based on orthologous groups

After merging the results from multiple runs with the join utility, you can classify the candidate sequences into orthologous subfamilies using the `selenoprofiles orthology` utility.

For example, continuing from the previous step where we merged profiles GPX and DIO into join_results/, you can run:

docker run --rm -v $(pwd):/mnt maxtico/selenoprofiles_container:latest \
    selenoprofiles \
    orthology \
    -i /mnt/join_results/GPX.ali /mnt/join_results/DIO.ali \
    -of /mnt/orthology_results

Refining selenoprotein predictions

After classifying candidate sequences with `selenoprofiles orthology`, you may want to filter out predictions that are not expected in a given lineage. This is especially useful to remove false positives or sequences that correspond to pseudogenes or retrotransposons.

The `selenoprofiles lineage` utility performs this filtering. It takes the .tsv files produced by orthology as input and outputs one filtered .tsv file per input, excluding non-expected genes based on lineage expectations.

Continuing our tutorial example:

docker run --rm -v $(pwd):/mnt maxtico/selenoprofiles_container:latest \
    selenoprofiles \
    lineage \
    -i /mnt/orthology_results/GPX.orthology.tsv /mnt/orthology_results/DIO.orthology.tsv \
    -o /mnt/lineage_results

Warning

When lineage utility is executed without -map option, the program uses a pre-installed module called *ncbi_db*. This happens because the tool needs to get the lineage for each species in the input file. The *ncbi_db* program requires a database file to infer the lineage. Thus, before running the lineage utility, you need to follow the following workflow:

Create a db file (tax.db) using ncbi_taxonomy_tree:

docker run --rm -v $(pwd):/mnt maxtico/selenoprofiles_container:latest \
    ncbi_taxonomy_tree \
    --makedb \
    -o /mnt/

1. Configure the ncbi_config file located in your home directory (e.g. ~/.ncbi_config) to point to the db file created in step 1. You can do this by changing the following line to the file:
```
ncbi_taxdb = /path/to/your/tax.db
```

Now you can run the lineage utility as shown above with a slight modification to the command:

docker run --rm -v $(pwd):/mnt -v ~/.ncbi_config:/root/.ncbi_config maxtico/selenoprofiles_container:latest \
    selenoprofiles \
    lineage \
    -i /mnt/orthology_results/GPX.orthology.tsv /mnt/orthology_results/DIO.orthology.tsv \
    -o /mnt/lineage_results \
    -map ncbi_db

Assessing selenoprotein annotations

Additionally, we can include in our workflow a final step to evaluate genome annotations, using `selenoprofiles assess`. This utility compares existing genome annotations with the Selenoprofiles predictions, producing a comprehensive overview of how well the genome is annotated for selenoproteins.

Countinuing our tutorial example, let’s assess how well the human genome is annotated for selenoproteins (note we require the genome annotation file genome.gff3 in addition to the genome sequence genome.fa):

docker run --rm -v $(pwd):/mnt maxtico/selenoprofiles_container:latest \
    selenoprofiles \
    assess \
    -s /mnt/homo_sapiens.gtf \
    -e /mnt/genome.gff3 \
    -f /mnt/genome.fa \
    -o /mnt/homo_sapiens.complete.tsv \
    -agg /mnt/homo_sapiens.aggregate.tsv

For more information regarding the selenoprofiles4 Docker, refer to the documentation: https://hub.docker.com/r/maxtico/selenoprofiles_container/