We recently got some shotgun sequencing results from a soil bacterium. And we have obtained some contigs which have some genes of interest.

Is there a way to automatically annotate the whole sequence (one single contig of around 25 kb size) and mark the genes on this stretch of DNA? I have never done this before so any help would be appreciated. The ultimate goal would be to know what genes are on this stretch of DNA and see if they work together in a pathway. But the first problem is:

How to annotate a stretch of DNA with many genes on it that would code for a protein/enzyme? so that I get a map of genes on this stretch of DNA. Thanks.


This is a soil isolate and we don't have a full genome sequence. Presumably, it is a Rhodococcus species, which might be similar. From the one gene we know, there are no exact homologs in the database so most probably it is a new strain. The strain works symbiotically with another strain which we are also working on and later I want to predict what proteins maybe involved in the catalysis of a specific compound. It is not a one step process so possibly multiple enzymes/proteins are involved. I tried UGENE and UGENE can identify multiple ORFs in this particular stretch, but there are hundreds of ORFS (on both strands) and I find it tedious to blast on NCBI one by one.

I didn't want too many questions in one post, so at the moment just focus on the identification of all the putative genes on this one contig would be good enough to start.

Thanks again.


1 Answer 1


There are a number of annotation pipelines that you could use to get fairly standardized annotation - Prokka has been around for a while (paper published in 2014) but is still used frequently. There's also Bakta, which may be better at catching short ORFs and providing more detailed functional annotation, but requires a fairly large database.

  • 1
    $\begingroup$ After I know about Prokka, I found it as a service on Galaxy webservice here. usegalaxy.org. Got the annotations done in no time. $\endgroup$
    – Irfan
    Dec 22, 2023 at 5:11

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