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

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.

go kegg eggnog-mapper
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updated by Biostar Biostar • written by zhangdengwei zhangdengwei

Hi Zhang,

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

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written by andres.firrincieli andres.firrincieli

1210 out of 2315 can be assigned to KEGG_ko

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written by zhangdengwei zhangdengwei

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

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written by andres.firrincieli andres.firrincieli

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

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written by Rogerio Ribeiro • Rogerio Ribeiro

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)

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written by andres.firrincieli andres.firrincieli

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