Why Is There Lack Of Go Terms With A Prokaryotic Genome.
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9.4 years ago
bob-lowlow ▴ 40

Hi I'm using Blast2Go to annotate and compare the core genome and the whole genome of a species of bacteria (Pseudomonas fluorescens). For the approximately 6000 genes only about 500 of them have GO terms, and 400 of them are in the core genome (which is approx 2000 genes). I was just wondering if anyone knew why this might be? I had heard before that Blast2Go was originally developed for use on prokaryotic genomes. Could this be affecting it?

Thanks

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9.4 years ago

GO annotations can be thought of as the accumulated knowledge for a certain organism. Model organisms have been studied a lot longer than others.

There are great many bacterial species moreover these often display great diversity between the genomes of the different strains of the same species. The lack of GO terms reflect the difficulty of annotating these genomes and perhaps the reduced research effort compared to model organism.

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Have you checked what your best blast hits are for things with no GO Terms as well? Lots of genes outside of the core genome for many prokaryotes are ORFans with very little, if any, annotation. That said I would expect you to get a bit better results than what you have reported.

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