The meaning and differences in TisType

[ruixuan-zhang]

Dear developer,

Good day. Thank you for your development and maintenance of this software.

I was wondering if you could explain about the definitions of different classes of TisType?

I see in README that TisType refers to the relative position of the TIS to annotated ORF of the transcript.

First, in my results, I got some predictions like 3' UTR, 5'UTR and Extended.

• Can I understand the class Extended in a way that if an assembled transcript from RiboSeq data is aligned to the annotated CDS region and the transcript is continuous without frameshift and extends outside of the annotated CDS, it is annotated as extended.
• While the 5'UTR and 3'UTR means that the TIS of a transcript is aligned to these untranslated regions and not assembled into the transcript of the CDS part (or not in the same frame)?

Second, I also got some Internal and Internal:CDSFrameOverlap

• I see CDSOverlap means the ORF overlaps with annotated CDS in another transcript in the same reading frame.
• Does Internal mean that a predicted ORF
  • locates within an annotated CDS (both ends locate within the annotated one)
  • is in different frame
• Does internal:CDSFrameOverlap means a predicted ORF locates within an annotated but in the same frame?

In the end, I am working on a virus genome with a high coding density. What if a predicted ORF, started in the upstream gene's CDS or 3'UTR region and ends in the downstream genes' CDS region in a different frame. What will the TisType be? Is that Novel or 3'UTR?

Thank you very much in advance!! Ruixuan