I am trying to annotate bunch of genomic sequences. I am using Blast2Go for this purpose. I have two main questions and sub questions that arise from them.
Question 1: The mapping step of Blast2go map several GO terms to a single blast result (single sequence). So a single sequence get assigned GO terms from Molecular function (MF), Biological process BP) and Cellular components (CC). ex: some sequences have 30,40 GO terms. A mixture of MF, BP and CC. So at the visualization step a single mapped and annotated sequence will appear in all three combined graphs for MF, BP and CC.
1.1 If one sequence get annotated as all three of these (MF, BP, CC), how can I know how many sequences out of my set of sequences are responsible for MF, BP or CC respectively ?
1.2 Is it possible for one sequence to do functions of MF, BP and CC ?
Question 2: Blast2go has Interproscan step. Which also find GO terms for the sequences of interest.
2.1 In the visualization step, does GO graphs use only GO terms from blast search mapping step? Doesn't it use GO terms from Interproscan?
2.2 Is there a better way to visualize these results?