Trinotate annotation

[keliyo]

Hello there,

I have performed a de novo transcriptome assembly with trinity, followed by RSEM and EdgeR to identify differentially expressed transcripts. And after that I have managed to determine that there are 200 significant features that are at least 4 fold differentially expressed. I have extracted these 200 transcript sequences and proceeded with trinotate annotation in order to know what are these 200 features.

My question is:

1) Is there any way that I can visualize these annotation results other than using TrinotateWeb that can aid in the summary of the annotation of these 200 features?


2) Does anyone know what could be the reason of more than 1 GO term was assigned to a particular transcript sequence?
For example: GO:0005829^cellular_component^cytosol`GO:0005634^cellular_component^nucleus`GO:0046872^molecular_function^metal ion binding`GO:0000978^molecular_function^RNA polymerase II core promoter proximal region sequence-specific DNA binding`

Thanks!!!

[TiborNagy]

1) I think the only other method is writing custom scripts.

2) Most of the genes has more than one GO terms, because:
- genes usualy codes more than one functional domains.
- GO is hierarchial
- GO has 3 separate starting points (molecular function, cellular component, biological function)