How do I associate a Unigene id with the GO ID ?
UniProtKB-GOA provides a UniGene to UniProtKB mapping (available at: ftp://ftp.ebi.ac.uk/pub/databases/GO/GOA/gp2protein/gp2protein.unigene.gz) Using either one of UniProtKB-GOA’s non-redundant species-specific files (Arabidopsis, chicken, cow, human, mouse, rat and zebrafish proteomes), or the UniProtKB-GOA UniProt gene association file, you should be able to parse out the appropriate set of GO terms for a set of Unigene ids.
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