3 Legitimacy of using gene ontology information

Before we propose subcellular-location predictors based on gene ontology (GO) information, in this chapter we will address some concerns about the legitimacy of using GO information for protein subcellular localization. There are mainly three kinds of concerns about using GO information: (1) Can the GO-based methods be replaced by a lookup table using the cellular component GO terms as the keys and the component categories as the hashed values? (2) Are cellular components GO terms the only information necessary for protein subcellular localization? (3) Are GO-based methods equivalent to transferring annotations from BLAST homologs? These concerns are explicitly addressed in the following sections. ...

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