2. Tutorial (Basic Settings)

Even via the command line, there are two ways to run SIRIUS. The first and simplest is to just call the program and provide i) your protein, and ii) the number of desired sequences, like so ./sirius MALEEINENSTERN 6.

The second way is to specify additional parameters via flags as described below.

1. --prot= string value

   • When using more than 2 arguments (like explained above), you need to provide SIRIUS with flags. With this flag, you can specify the protein as mentioned above (--prot=MALEEINENSTERN).

2. --n= integer value > 2

   • Specify the number of desired synonymous genes.

3. --hard_rscu= boolean value (true/false) [Default: false]

   • Specify if you would like to provide a hard cut-off for codons with an RSCU value under this threshold. Switching this flag to true requires you to also specify the following:
     • --codon_usage_fpath= string value.
       • Path to the .csv file containing amino acid codes, their codons, and the respective RSCU values.
     • --rscu_threshold= positive floating point value [Default = 0.5]
       • Codons with an RSCU below this value will be completely excluded from the output genes. If not provided by you, a default value is used.

A simple execution with flags may look like:

./sirius --prot=MALEEINENSTERN --n=3 --hard_rscu=true --codon_usage_fpath=my_codon_usage.csv which will use a default --rscu_threshold.

Proceed to advanced settings to learn more.