How is prodigal modified?

[Haiyue Meng]

Hi AMPSphere developers,

In the paper I see that "we used a modified version of Prodigal to predict smORFs (33–303 bp) from contigs", can you please share how did you modify prodigal?

My guess is that update MIN_GENE/MIN_EDGE_GENE/MAX_SAM_OVLP these 3 macros to 30, am I correct?

[Luis Pedro Coelho]

Dear Haiyue Meng,

Yes, that is correct. This is available with older versions of macrel (https://macrel.readthedocs.io/en/latest/install — the version for the paper was 0.5). If you install those older versions, you should have the prodigal_sm command available to you.

Note that in the meanwhile, we have switched to using pyrodigal which is simpler, so newer versions of macrel do not use this anymore.

Best, Luis

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Luis Pedro Coelho | Queensland University of Technology | https://luispedro.org

https://orcid.org/0000-0002-9280-7885