SEA-PHAGES | Help with Annotating Direct Terminal Repeats

Link to this post \| posted today, 14:32
fogartym1	I am finishing up annotation on Phage Vitaenoii and need some help with the annotation in the direct terminal repeat area. Vitaenoii has 1206 bp direct terminal repeats (DTRs). At the 3' end of the genome the last called gene is 486 bp. 406 bp of the gene is within the DTR with the stop codon about 80 bp upstream of the DTR. Genemark and Glimmer call the gene with good confidence and there are 11 members of the pham (all CS4 phages). My sense is to call the gene, but it will mean that the DTR is annotated differently at the beginning and end of the genome. Is this reasonable? I have attached an image of the coding potential for each end of the genome. Thanks Marie Edited today, 14:35 144Kb

Link to this post | posted today, 14:32

I am finishing up annotation on Phage Vitaenoii and need some help with the annotation in the direct terminal repeat area.

Vitaenoii has 1206 bp direct terminal repeats (DTRs).
At the 3' end of the genome the last called gene is 486 bp. 406 bp of the gene is within the DTR with the stop codon about 80 bp upstream of the DTR. Genemark and Glimmer call the gene with good confidence and there are 11 members of the pham (all CS4 phages).
My sense is to call the gene, but it will mean that the DTR is annotated differently at the beginning and end of the genome. Is this reasonable?

I have attached an image of the coding potential for each end of the genome.
Thanks
Marie

Edited today, 14:35

Link to this post \| posted today, 15:02
cdshaffer	yes. The genome is going to circularize after entry, at which point there is only one copy of the repeat within the genome. This means that annotations of the linear genome will always have the possibility of this kind of quirk. In addition, if you annotated a partial gene at the start of the genome it would cause all kinds of issues for the all the computational checks and make handling the genome much more labor intensive, so the best approach is as you suggest. Annotate the copy that is the full intact gene at the end and do not annotate the partial gene at the beginning.

Link to this post | posted today, 15:02

cdshaffer

yes. The genome is going to circularize after entry, at which point there is only one copy of the repeat within the genome. This means that annotations of the linear genome will always have the possibility of this kind of quirk. In addition, if you annotated a partial gene at the start of the genome it would cause all kinds of issues for the all the computational checks and make handling the genome much more labor intensive, so the best approach is as you suggest. Annotate the copy that is the full intact gene at the end and do not annotate the partial gene at the beginning.

Link to this post \| posted today, 15:04
fogartym1	Perfect, thanks so much

Link to this post \| posted today, 15:06
debbie	Chris and Maria, Excellent choices! Only call one. And do not call a wrap round version. debbie

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Help with Annotating Direct Terminal Repeats