Question: Genome Annotation of a new bacterial strain
gravatar for Paul
4 months ago by
Paul70 wrote:

I have a new bacterial strain which I assembled using SPADES and scaffolded it using SPADES. Now to annotate the scaffolds, I used RAST. RAST has given me 8000 genes. I tried to annotate the genes using RAST. Out of 8000 genes, only 1497 genes got annotated using RAST.

Could you please suggest me a way to annotate the whole 8000 genes.

ADD COMMENTlink modified 3 months ago by Biostar ♦♦ 20 • written 4 months ago by Paul70

How big is your genome? 8000 seems like a high number for a bacteria. Chances are most of those predicted CDSs are junk.

Try annotation with Prokka and see if you get comparable results.

ADD REPLYlink written 4 months ago by jrj.healey12k

How many contigs do you have? Did you check the overall assembly quality (e.g. with QUAST) and/or degree of potential contamination (you should always check ALL your assemblies with checkm)?

I agree with jrj.healy that you should try prokka. It's the by far best automatic annotation program I have seen yet.

Leaving potential quality considerations aside (8000 genes DOES sound a lot though), keep in mind that you can't expect a 100% annotation rate even in the best case. You will frequently end up with more than 50% unannotated "hypothetical genes". And the more distant related your new Isolate is to any known reference genomes (--> The "newer" the organism seems to be), the less genes can be successfully annotated based on references.

ADD REPLYlink modified 4 months ago • written 4 months ago by JV380
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