Can someone provide me some information about the main method used to predict the inferred electronic annotations in Gene Ontology?
This paper ( http://bib.oxfordjournals.org/content/12/6/723.full ) says that the majority of IEA-annotations come from the GOA-database annotation pipeline, which is based on four sources: UniProtKB/Swiss-Prot Keywords2GO, EC2GO, HAMAP2GO and InterPro2GO. For more information, check out their paper: http://nar.oxfordjournals.org/content/37/suppl_1/D396.full
Phillip is spot on in his reply. You can see the breakdown of annotations by different sources/methods in the latest UniProt release here: http://www.ebi.ac.uk/GOA/uniprot_release.html
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