Link to this post | posted 12 Jul, 2019 22:01

debbie

Hi Jordan, I would call both genes, and I would call the second one to include all of the coding potential, even though it is a huge overlap. Then I would carefully look to see if the two pieces have functional domains that I could call separately. If you get stuck, ask again. also, what does the sequence look like that causes this gene to be disrupted. You called it a deletion, is it a single base? We should probably ask for confirmation of the sequence.

Link to this post | posted 09 Jul, 2019 19:58
debbie	I just annotated Undlulmathi (Zulu for giraffe!) and am only willing to annotate the "G" of the tail assembly chaperone. It is bigger than most "G" genes, so I am betting that is significant. I am not calling the next gene a TAC and there is NO obvious slippery sequence to call. I will modify the TAC calls of Cuke and FowlMouth soon (but not now). debbie 7-9-19

Link to this post | posted 25 Jun, 2019 15:13
debbie	Steve, I am late to this game, but I have not had any trouble accessing Aragorn. debbie

Link to this post | posted 19 Jun, 2019 01:43
debbie	Alison, We can do that! We will need to complete an MTA and then we can send it to you (from the NRRL collection). Be sure that the legal contact and shipping address is correct on your institution page. Thanks, debbie

Link to this post | posted 03 Jun, 2019 20:11
debbie	Recently, we learned that all siphos do not need to have one or both of the TACs. So it would not be wrong to omit the call without evidence.

Link to this post | posted 03 Jun, 2019 19:48

debbie

Maria, If there is a frameshift, it is a -1 because the second gene is -1 from the first. However, I don't see a slippery sequence to call in FuzzBuster. My quick look at HHPred in PECAAN, says you might not even want to call these things TAC. If you are using PECAAN, you might want to re-run your HHPred in PECAAN because it is dated Jan, 2019. I believe the databases used around that time were not complete. debbie

Link to this post | posted 28 May, 2019 12:52

debbie

Fernando, You have called the frameshift exactly correctly. It is a -1 frameshift. The "G" gene is annotated as 14986 - 15363, product is "tail assembly chaperone. The "T" gene is annotated as 14986 - 15785, with 2 regions (14986 - 15339, 15339 - 15785), product is tail assembly chaperone. So it sounds like what confused you is that the "g" gene 'happened to be located in the top frame of the six-frame translation output". and you your real question is where would the -1 frame be, in relationship to that. As you can now see, it is the bottom displayed frame. Is that what you were asking? debbie

Link to this post | posted 24 May, 2019 16:39
debbie	Fernando, Please send me your DNA Master file and I can show you. If you make sure each region is divisible by 3 it will show you where to cut it. If this is a -1 frameshift (most certainly it is), the last nucleotide of region 1 is the first nucleotide of region 2. Your frame jumping question is not easy to follow when the ribosome is really slipping backwards. debbie

Link to this post | posted 20 May, 2019 19:33

debbie

Dear SEA-PHAGES faculty, Have you see phage DNA appear as a smear on an agarose gel? There are particular instances in which DNA modification can lead to degradation in the gel buffers, such that even undigested genomic DNA appears as a smear. It’s possible that you’ve observed it but not necessarily submitted the DNA for sequencing. We would like to hear whether or not you’ve seen this. We’ve opened up a Forum at seaphagesdb.org, and would like to encourage you to indicate with which phages you saw this (with pictures if you have them) or point to a phage pages on phagesdb.org if the data are posted there. But we’d also like it if you could post a note saying that you have never seen this, if that is the case. If you have further questions, don’t hesitate to contact me. Thanks! debbie

Link to this post | posted 15 May, 2019 18:26

debbie

Sally, Technically, we can call a single TMD if 2 programs find it. I would not be opposed to calling them both Hypothetical Proteins. I just looked at these in phamerator. These 2 genes are found in a region of high nucleotide pairwise similarity (the purple color inbetween). However, the first of these 2 genes is a member of 3 different phams. Are they all calling different things, or is this a case of small genes not meeting alignment cut-offs to make it into the same pham? debbie