Annotation and GO Enrichment

recommended process for annotating genes for Roberts Lab UW: https://robertslab.github.io/resources/bio-Annotation/ If you look at the GO and GOslim sections, the process is like this: Use SwissProt IDs to query UniProt, via Python script. Map GO IDs to GOslims using packages available in the R programming language (specifically, GSEAbase and GO.db). This process uses the most up-to-date GO/GOslim info, since it’s utilizing the GO Consortium generic goslim obo file.

If applicable but if you have unannotated reference genomes (or perhaps genomes that need an updated annotation) easel (https://gitlab.com/PlantGenomicsLab/easel) and maybe EnTAP (https://gitlab.com/PlantGenomicsLab/EnTAP) might be good to look at. These software are from a UConn lab, and they’ve built a program around reference genomes and annotation. GOs could be pulled from the annotation. (edited)

GitLabGitLab PlantGenomicsLab / EASEL · GitLab GitLab.com

GitLabGitLab PlantGenomicsLab / EnTAP · GitLab GitLab.com