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

Link to this post | posted 07 May, 2019 19:19
debbie	Kristen, While I agree the currently called ribosomal slippage is not a stellar example, I don't think the placement of your proposed slippage works (because you are slipping out of the first frame too soon). I think we are approximately at the right place if there is indeed a frameshift. If you look at Powerball, the GGGGACT is not there…….. Kristen - I'll ask Welkin for her in put. debbie

Link to this post | posted 24 Apr, 2019 18:25

debbie

Christos, Try the following things, one may do the trick. If not send it to me and I will try to make it work. At the feature table, go to the left sequence tab. Once in the window, above the sequence, click on the button "raw". Recreate your documentation. Go to documentation, the click on recreate. Save the file as a new name and see if it works. If you do need my help, what is he trying to export? debbie

Link to this post | posted 19 Apr, 2019 18:45
debbie	Sara, Nope. Sorry for the confusion. I think that peak is a gene (7165-7272). I just have no confidence it is the T of the G/T frameshift, so I would not assign a function to it.

Link to this post | posted 18 Apr, 2019 13:27

debbie

Sara, This is a timely question. This summer Welkin learned that siphoviridae do not have to have 2 tail assembly chaperone genes. Some can have one. Our evidence for phage Laila is that it has one. When we originally called these genomes, we assumed 2. I think that little gene between the TAC and TMP, gene 14, is real, but not necessarily a tail assembly chaperone (and therefore a hypothetical protein). Make sense? thanks for the question! debbie