SEA-PHAGES | Forward gene with good evidence among reverse genes

Link to this post \| posted 01 Mar, 2017 17:16
beckiebortz	This question concerns a Gordonia phage and all other phages in its cluster are draft. Essentially there is a forward gene that has good coding potential among a group of reverse genes. My students are inclined to call the forward gene but there is confusing evidence. There is a reverse gene called by Glimmer-only in the same region as the forward gene and the confusion is somewhat compounded by gene numbers that differ in DNA master and Phamerator. Our decision at this point is to delete the reverse Gene 42/43 (29120-29410) and perhaps make adjustments to the starts of the earlier reverse gene (28972-29163R) and the forward gene (29243-29386) based on BLAST hits. The later reverse gene should remain as auto-annotated. Does this seem like a legitimate call or have we missed some critical piece of evidence? Edited 01 Mar, 2017 17:45 116Kb 191Kb 102Kb

Link to this post | posted 01 Mar, 2017 17:16

This question concerns a Gordonia phage and all other phages in its cluster are draft. Essentially there is a forward gene that has good coding potential among a group of reverse genes. My students are inclined to call the forward gene but there is confusing evidence. There is a reverse gene called by Glimmer-only in the same region as the forward gene and the confusion is somewhat compounded by gene numbers that differ in DNA master and Phamerator. Our decision at this point is to delete the reverse Gene 42/43 (29120-29410) and perhaps make adjustments to the starts of the earlier reverse gene (28972-29163R) and the forward gene (29243-29386) based on BLAST hits. The later reverse gene should remain as auto-annotated. Does this seem like a legitimate call or have we missed some critical piece of evidence?

Edited 01 Mar, 2017 17:45

Link to this post \| posted 01 Mar, 2017 18:56
welkin	Hi Beckie— I love the Gordonia phages! These areas flanking the integrase seem particularly plastic and so it doesn't surprise me that the normal guidelines aren't holding up. Based on your GenemarkS output (which I think is the most compelling evidence you've got here) I want to keep the forwards 43 that is in the middle of that reverse operon. I also think you are right; you make sure that you call the reverse gene to start at 29163 and no longer to accommodate the forwards gene, and delete the other reverse gene that occupies the same space as the forwards gene. I could be persuaded to change my mind though, if you run them all through HHPred and find functions for the reverse gene that you propose to delete. -Welkin

Link to this post | posted 01 Mar, 2017 18:56

welkin

Hi Beckie— I love the Gordonia phages! These areas flanking the integrase seem particularly plastic and so it doesn't surprise me that the normal guidelines aren't holding up.

Based on your GenemarkS output (which I think is the most compelling evidence you've got here) I want to keep the forwards 43 that is in the middle of that reverse operon. I also think you are right; you make sure that you call the reverse gene to start at 29163 and no longer to accommodate the forwards gene, and delete the other reverse gene that occupies the same space as the forwards gene.

I could be persuaded to change my mind though, if you run them all through HHPred and find functions for the reverse gene that you propose to delete.

-Welkin

Link to this post \| posted 29 Mar, 2017 18:39
akoga	Becky, I looked at this same region in asapag a few days ago. While our auto-annotation did not call the genes in such a grossly overlapping way, we were still thinking we should delete the same reverse gene (44 for us) as you have decided to delete. It has NO coding potential and results in an overlap of the forward and reverse gene starts. Like yours, our next gene is a forward gene, which had Start #2 called. It looks like all the DN drafts have the earlier start conserved as well (longest ORF). For us, that is a TTG with a decent SD score. Did you decide to extend that forward gene by using the first start?

Link to this post | posted 29 Mar, 2017 18:39

akoga

Becky,
I looked at this same region in asapag a few days ago. While our auto-annotation did not call the genes in such a grossly overlapping way, we were still thinking we should delete the same reverse gene (44 for us) as you have decided to delete. It has NO coding potential and results in an overlap of the forward and reverse gene starts. Like yours, our next gene is a forward gene, which had Start #2 called. It looks like all the DN drafts have the earlier start conserved as well (longest ORF). For us, that is a TTG with a decent SD score. Did you decide to extend that forward gene by using the first start?

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Forward gene with good evidence among reverse genes