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Forward or reverse gene?
Link to this post | posted 25 Mar, 2019 23:19 | |
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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 | |
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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 |
Link to this post | posted 26 Mar, 2019 15:34 | |
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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 | |
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I still like my little gene call. This area is definitely tricky. |