Recommended method for finding operons?

[jolespin]

This could be great for identifying operons. Do you have any examples of using this tool to identify common operons? For example, nif operons or others involved in nitrogen fixation.

[Robaina]

Yeah, exactly, that's a great use case. I have used Pynteny before to search for the Nif operon, also helping to tell paralogs apart from homologs.

I created a small case study to illustrate how this works.

[jolespin]

Incredible resource! Is there any way to use the synteny detection from existing HMM results? For example, I've already run PyHMMSearch and PyKOfamSearch w/ PGAP and thinking it would be useful to screen existing annotations.

I'm wondering how feasible it would be to incorporate a module whose input was something like the following:

# input.tsv
id_genome, gene_name, chromosome, start, end, strand

Perhaps some command like this:

pynteny synteny \
    --synteny_struc ">nifH 0 >nifD 0 >nifK" \
    --data_batch input.tsv \
    --best_hmm_wins --outdir results/A_strict_nifHDK/<genome>

or even for larger batches:

# synteny.tsv
id_synteny, synteny_structure, ordered

pynteny synteny \
    --synteny_batch synteny.tsv \
    --data_batch input.tsv \
    --best_hmm_wins --outdir results/A_strict_nifHDK/<genome>