Link to this post | posted 26 Mar, 2019 19:01
debbie	Cool!

Link to this post | posted 26 Mar, 2019 19:00

debbie

Joe, I think you are confusing apples and oranges here. The 'standard code" settings have no effect anywhere in auto-annotation. Also if you have chosen ATG, GTG, and TTG start codons in the Translation tab of the Local Settings in your preferences, DNA Master will display them. You can select "Bacteria and Plant Plastid Code" in the New Features Tab of the Local Settings. Is that what changes? What is changing on you? debbie

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

Link to this post | posted 26 Mar, 2019 08:40
debbie	Philippos, Hi. No, I would not call auto-annotated gene 123, but instead call the longer gene you describe (it is a DNA methylase, so that should convince you). In addition, don't miss the next forward gene, because it too is a DNA methylase. See my attached frames window. Check out the differences in the auto-annotation…. 25Kb

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 21 Mar, 2019 11:53

debbie

Sarah, After preliminary work with host range experiments, I am finding that the best way forward is to find phages on hosts that you would like to test. Until you are familiar with a host, the testing of additional hosts with known phages can be problematic. By that I mean, if you don't have a phage that infects each host, how do you know that a phage that you are testing can infect that host (or that that infection is detectable)? If it does, great! But if it doesn't, is your test valid (without a positive control)? So my recommendation going forward is to add some new hosts, go phagehunting on that host, then begin the host range testing. Does that make sense?

Link to this post | posted 18 Mar, 2019 18:45
debbie	Veronique, I agree, I see no function to call for the second gene in question. and I would call the first one the "capsid maturation protease and MuF-like fusion protein".

Link to this post | posted 15 Mar, 2019 02:54
debbie	Erin, I don't think it has to have 2 domains, it just has to have 1 convincing one. The problem is that one program doesn't have adequate sensitivity. So if there is only one, we want it verified by 2 sources. Without the option to 'verify' a transmembrane domain with a second program, let's not add it as a function.

Link to this post | posted 15 Mar, 2019 02:41

debbie

Evan, In this case you can't ignore the comparisons, not can you ignore that there is a gap. If we could say that coding potential is always weighted in a particular way for every gene, we could write the program and stop doing this manually. BUT there are too many factors and they are not weighted the same in each instance (gene), so it requires human evaluation. At least for now…. Do not exclude this gene. (until you have evidence to do so.)

Link to this post | posted 15 Mar, 2019 01:22
debbie	No. it is dependent on the random 'sample' that it used. therefore, the patterns picked up work well for big genes, but 'fall apart' for small ones. Yes, the sequence of the gen is the same, but the random samples used to measure against are different. They are even different for the same genome, hence thy are based on a random sample of the genome.