few genes were annotated to GO terms using online eggnog-mapper

Question

[zhangdengwei]

Hi all,

I was using online eggnog-mapper (http://eggnog-mapper.embl.de) to annotate a list of bacterial genes. But I found only 11 out of 2315 genes were successfully annotated to GO terms. All genes had hit on eggNOG ortholog. I don't why only few genes had GO term. Any explain or suggestion would be greatly appreciated. Thanks in advance.

[andres.firrincieli]

Hi Zhang,

How many genes have been assigned to KEGG orthology (KO)?

[zhangdengwei]

1210 out of 2315 can be assigned to KEGG_ko

[andres.firrincieli]

At least we know that your protein are assigned to OG with a functional annotation term (KO). It could be that none of the OG have a GO term. One way to assign GO to your proteins is to use the standalone version of InterproScan

[Rogerio Ribeiro]

Hi. I was also looking to annotate my transcriptome (genome-guided). I used InterproScan + pannzer2, and extracted the GO annotations from only pannzer. Just out of curiosity, using InterproScan wouldn't mean most of my GO terms will belong to the MF category? Thx in advance

[andres.firrincieli]

Hi,

I never checked this but it should give you back all the GO terms (MF, BP, and CC) associated to that particular protein; see: IPR001095 (bottom page)