Welcome to the forums at seaphages.org. Please feel free to ask any questions related to the SEA-PHAGES program. Any logged-in user may post new topics and reply to existing topics. If you'd like to see a new forum created, please contact us using our form or email us at info@seaphages.org.
Recent Activity
All posts created by debbie
| Link to this post | posted 28 Aug, 2025 14:24 | |
|---|---|
|
Ombeline, Hi. I don't have time to troubleshoot, but I will make your profiles for you. Would you send me well labeled files and I will get them back to you? Best, debbie |
Posted in: DNA Master → Can´t make profile
| Link to this post | posted 14 Aug, 2025 17:29 | |
|---|---|
|
|
Rick, Very nice. Also a very fun area to think about. Cluster FK are not the only ones to have these. Cluster Bs, and Os also. Any categorization of these would be helpful! debbie |
| Link to this post | posted 11 Aug, 2025 15:16 | |
|---|---|
|
|
Hi Randy, This is going to take a bit of time to check. And i don't have that time, so maybe I can provide enough info' to get you started. Historically, it was thought that all sipho have TACS, canonically directly upstream of the tape measure. There is now reports that the genes are present, and do not have to be beside each other. And that not all sipho have TACs. There is also evidence that the 4 nucleotide sequence of XXXY can constitute a slippage (if they are in the 'right spacing' of the reading frames). That is part of the evaluation that can occur. Having the numerous cluster members to compare will also be informative. I don't know what you meant about a second slippage site. You are correct to look more closely. debbie |
Posted in: Frameshifts and Introns → TAC frameshifts in CF
| Link to this post | posted 29 Jul, 2025 17:26 | |
|---|---|
|
|
Thanks Chris! |
Posted in: Cluster AS Annotation Tips → deoxycytidylate deaminase OR nucleoside deoxyribosyltransferase.
| Link to this post | posted 28 Jul, 2025 20:36 | |
|---|---|
|
|
I checked this out and realized I needed to gain some basic (very basic) biochem) to my understanding: Nucleoside Deoxyribosyltransferase (NDT): Function: NDT transfers deoxyribose from one nucleoside to another, effectively swapping bases. Deoxycytidylate Deaminase (DCTD): Function: DCTD specifically deaminates dCMP to dUMP, removing an amine group. My question is what are the residues/domains that could help to differentiate these? Maybe, my question is how do you recognize a deaminase domain vs a transferase domain? just maybe… debbie |
Posted in: Cluster AS Annotation Tips → deoxycytidylate deaminase OR nucleoside deoxyribosyltransferase.
| Link to this post | posted 09 Jul, 2025 13:53 | |
|---|---|
|
|
Julie, Hi. I have no data to help with this one. Best, debbie |
| Link to this post | posted 25 Jun, 2025 14:39 | |
|---|---|
|
|
Ping, I think a titer of any number is sufficient if you have purified the bacteria such that residual phage from somewhere outside of the cell is removed. I would not evaluate this is a vacuum. are the cells homo-immune to that phage infection. Build the evidence and then see what it tells you. We do not have empirical numbers, but you can collect that data. (And then we would for each phage.) Best, debbie |
Posted in: Lysogeny/Immunity → Liquid phage release assay
| Link to this post | posted 13 Jun, 2025 01:42 | |
|---|---|
|
|
Lee, It sounds correct to me! XXXYYYZ is always a winner! debbie |
Posted in: Frameshifts and Introns → TAC Frameshift in BJ and BN
| Link to this post | posted 05 Jun, 2025 05:53 | |
|---|---|
|
|
Fred (and all), We are aware that the GeneMark server is down. An email has been sent to notify the owners that it is down and requesting that it be restarted. debbie |
Posted in: Annotation → GeneMark Server Connection
| Link to this post | posted 28 May, 2025 15:01 | |
|---|---|
|
|
Hi all, So if your file is live in GenBank, it will have the family classification stated there. You ca n use it. We could try to keep up as we enter things into GenBank, but honestly, ICTV can't keep up with us. Best, debbie |