bioinformatics - Main methods used to predict functional annotations in GO

I believe the most common source of electronic annotations comes from analysis of peptide sequences. A collection of InterPro to GO mappings were created manually and can generate GO annotations. DNA binding domains of transcription factors would be given "DNA binding" GO annotations say.

This method has its flaws - if the domain detected has evolved away from the function used for the Interpro to GO listing, there is a potential for error in this method.