maxtico/seblastian repository overview

⁠SECISearch3 / Seblastian program for prediction of eukaryotic SECIS elements and selenoproteins

The workflow is described at:

Note that a webserver with these programs is available at: https://seblastian.crg.es/⁠

• After downloading this container via docker pull, run this to inspect command line options:

 docker run maxtico/seblastian python /Seblastian/Seblastian.py -h

• To use docker to run SECISearch3 on TARGET.FA nucleotide fasta file and write output in OUTPUT/ folder, both located in the current folder, use:

 docker run -v $(pwd):/data maxtico/seblastian python /Seblastian/Seblastian.py -t /data/TARGET.FA -o /data/OUTPUT -SS

• To run the full Seblastian pipeline using a built-in dataset of known selenoproteins:

 docker run -v $(pwd):/data maxtico/seblastian python /Seblastian/Seblastian.py -t /data/TARGET.FA -o /data/OUTPUT2

• To run the full Seblastian pipeline using your custom protein database (i.e. use uniref or another comprehensive database to allow prediction of novel selenoproteins):

 docker run -v $(pwd):/data maxtico/seblastian python /Seblastian/Seblastian.py -t /data/TARGET.FA -o /data/OUTPUT3 -d /data/MY_DB_FILE.FA

For other uses, see command line options as mentioned above.