SEA-PHAGES | Forward or reverse gene?

Link to this post \| posted 25 Mar, 2019 23:19
ptsourkas	Gene 103 (forward frame 3, 61983-62291) in cluster J phage NihilNomen is called by Glimmer and GeneMark (the GeneMark in DNA Master) and has strong coding potential for part of its length. While ordinarily this would be a no brainer, there is an ORF in reverse frame 1 (62040-62480) with equally strong coding potential and called by host-trained GeneMark.hmm and GeneMark S. The two genes overlap, but not completely (see attached figure). In terms of homology matches, gene 103 has 6 matches to cluster J phages, while the reverse ORF has none. Call both genes? Or just gene 103? 74Kb

Link to this post | posted 25 Mar, 2019 23:19

Gene 103 (forward frame 3, 61983-62291) in cluster J phage NihilNomen is called by Glimmer and GeneMark (the GeneMark in DNA Master) and has strong coding potential for part of its length. While ordinarily this would be a no brainer, there is an ORF in reverse frame 1 (62040-62480) with equally strong coding potential and called by host-trained GeneMark.hmm and GeneMark S. The two genes overlap, but not completely (see attached figure).

In terms of homology matches, gene 103 has 6 matches to cluster J phages, while the reverse ORF has none.

Call both genes? Or just gene 103?

Link to this post \| posted 26 Mar, 2019 08:27
debbie	Philippos, Hi. I took a look at this area and I would not call that or the next reverse gene(see Phamerator). Instead I wold add a small ORF in the forward direction between 103 and 105. If you look at your auto-annotation, my auto-annotation, and Phamerator, I think there are differences in this region across all 3. Which means basically there is poor coding potential all-around. Note: I see no strong coding potential in the reverse frames. The red dotted lines on a GeneMark graph are demonstrating an order of 2 (patterns of 2 nucleotides at a time), which most of the time amounts to noise. So if you look at your example, the black line is poor coding potential (order of 4). Make sense? debbie Edited 26 Mar, 2019 08:28 26Kb

Link to this post | posted 26 Mar, 2019 08:27

debbie

Philippos,
Hi. I took a look at this area and I would not call that or the next reverse gene(see Phamerator). Instead I wold add a small ORF in the forward direction between 103 and 105. If you look at your auto-annotation, my auto-annotation, and Phamerator, I think there are differences in this region across all 3. Which means basically there is poor coding potential all-around.
Note: I see no strong coding potential in the reverse frames. The red dotted lines on a GeneMark graph are demonstrating an order of 2 (patterns of 2 nucleotides at a time), which most of the time amounts to noise. So if you look at your example, the black line is poor coding potential (order of 4). Make sense?
debbie

Edited 26 Mar, 2019 08:28

Link to this post \| posted 26 Mar, 2019 15:34
ptsourkas	Hi Debbie, and thanks for looking into this. I looked into the small forward ORF you mentioned but I feel the coding potential for that one is very weak, and it is more likely that gene 105 should be called long instead (which would fill the gap somewhat).

Link to this post \| posted 26 Mar, 2019 18:52
debbie	I still like my little gene call. This area is definitely tricky.

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Forward or reverse gene?