Question: Genome Annotation of a new bacterial strain
gravatar for Paul
16 months ago by
Paul80 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 15 months ago by Biostar ♦♦ 20 • written 16 months ago by Paul80

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 16 months ago by Joe16k

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 16 months ago • written 16 months ago by JV400
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 826 users visited in the last hour