Some viruses use genetic codes other than standard genetic code. These scripts could work on Linux server with Biopython (python) and Prodigal (worked for v2.6.3) Sequences with length > 10k and GC content 50 % are selected as candidate sequences.

Usage

1

python select_gc_and_length_cutoff_seq.py all_virus_seq_split recoding

all_virus_seq_split is a directory containing fasta files of single viral sequences

recoding is a directory generated to store candidate sequences to use an alternative genetic code

2

python batch_run_gff_output_genetic_code.py recoding recoding_file genetic_code_rating.txt

recoding is mentioned aboved

recoding_file is a output directory containing prodigal gff files

genetic_code_rating.txt is a file to summarize the scores of alternative genetic codes and the selection of genetic codes

3

python batch_run_prodigal_with_recoding.py all_virus_seq_split recoding_rating_out.txt prodigal_out

all_virus_seq_split is above-mentioned

recoding_rating_out.txt is above-mentioned

prodigal_out is going to be generated, storing the prodigal protein/gene files

Prodigal didn't work for sequences less than 20k with -p single option, however, it is needed for changing the genetic codes in Prodigal. In the second and the third scripts, I doubled the sequences less than 20k, this doesn't change the codon usage of sequences and Prodigal worked for it. When Prodigal predicts these doubled sequences, the output is the same set of proteins/genes, then I remove the duplicated part of files.

References

1. https://www.nature.com/articles/s41564-021-00928-6 (the standard to determine alternative genetic codes of viruses)
2. https://github.com/hyattpd/Prodigal (Prodigal)
3. https://academic.oup.com/bioinformatics/article/25/11/1422/330687 (biopython)