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Recent Activity
JustinA posted in Plaques appear on spot test, don't appear in titer
Viknesh Sivanathan posted in Plaques appear on spot test, don't appear in titer
JustinA posted in Plaques appear on spot test, don't appear in titer
Viknesh Sivanathan posted in Plaques appear on spot test, don't appear in titer
RyanWheeler posted in Plaques appear on spot test, don't appear in titer
All posts created by debbie
| Link to this post | posted 11 Nov, 2020 20:57 | |
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Hi Christina and Nikki, I think I would first rely on the coding potential and call the longer version of 71. While I would likely fill in this space with genes of the 4 bp overlap variety when I didn't have compelling coding potential choices, i like the coding potential better here. While this may not help (but I haven't looked lately), there is a paper with mass spec for the genes of some of the Cluster J phages. I am sure if we had evidence of the 2 genes for the phages in that paper, we would have called them. From my quick glance, we did not. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0069273 debbie |
Posted in: Choosing Start Sites → LO or insert gene in J cluster Beem
| Link to this post | posted 07 Nov, 2020 18:50 | |
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To fix a "Key Violation" error, this should work: Make yourself a backup directory on your desktop (name it something like OldRecentFiles) Then browse to C:/ProgramFiles/DNA Master/DMDB There will be a bunch of files in there that all start with "RecentFile" Move all of those into the new backup directory on your Desktop just in case. Then restart DNA Master. It will say that it can't find the RecentFile DB files, and will download new copies of them (this should happen automatically). If not, click the button marked "Download from FTP site" at the upper right hand corner of the table that pops up. You can then discard the files that you moved out. |
Posted in: DNA Master → Key Violation
| Link to this post | posted 22 Oct, 2020 01:06 | |
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Thanks Chris! |
| Link to this post | posted 21 Oct, 2020 19:12 | |
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Hi Parks, I am not sure, but wanted to give you some more to think about or do. See the attached picture and look at the sequence at 9731. A more canonical slippage, but really upstream of the stop of the "G" part of the G/T gene. What would be helpful is to check out the other CZ1s and see if a consensus sequence is apparent in that place. Alignments are in order! I do like the sequence, but I don't like how upstream it is…. need more info and to think about it. debbie |
76KbPosted in: Frameshifts and Introns → CZ1 Tail assembly proteins
| Link to this post | posted 09 Oct, 2020 17:20 | |
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Sorry for the delay in this response. I know of no fool-proof way to force induction. The literature describes UV and mitomycin C as agents. We have found that spotting one culture (or the supernatant of one) on a lawn of another will identify released phage of a prophage. I think that is all i have for now. debbie |
| Link to this post | posted 06 Oct, 2020 20:17 | |
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When documenting Blast-Start, you will want to address that you are choosing a start that aligns to others' calls. The % coverage is asking you to note that you have % identities? Did you match the whole length of the protein or just a part of it. It should also include that you matched the start 1:1 (or whatever the alignment is). The note in the Bioinformatic Guide about % alignment in the HHPred results is : "%alignment" here refers to the % of the query protein that is aligned to the target sequence. you will need to calculate this by hand, as HHPred does not report it as a number for you, it merely reports the length of your sequence that is included in the alignment. Divide this number by the full length of your query sequence. Estimates of that % would be great! |
Posted in: Notes and Final Files → Coverage and Alignment
| Link to this post | posted 26 Sep, 2020 19:37 | |
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Hi Michael and all, Phamerator is undergoing a rather big update this weekend. It will take a bit of time for the remaining databases to catch up. This forum explains. https://seaphages.org/forums/topic/254/ debbie |
Posted in: Starterator → Pham 36129 report not found in Starterator
| Link to this post | posted 24 Sep, 2020 11:46 | |
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Hi Steve, This is likely due to the wild fires in California. It appears that folks can be back on campus, but if the Lowe lab can't get to their servers, tRNA-ScanSE is in jeopardy. debbie |
Posted in: tRNAs → tRNAScan-SE Down-ish?
| Link to this post | posted 20 Sep, 2020 19:16 | |
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We have more experimental data for -1 frameshifts. So we will call the -1 until we can do an experiment to differentiate. debbie |
Posted in: Frameshifts and Introns → Frameshift K6
| Link to this post | posted 11 Sep, 2020 20:53 | |
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Hi all, I think the fix is easy. I believe - if you are clicking on DNA Master.exe –you are clicking on the DNA Master installation program. That is not the one that you want. Go to C: -> Program files -> DNA Master folder and look for the DNAMas.exe file which will run DNA Master. Be sure to check that you are running as administrator. Let me know, debbie |
Posted in: DNA Master → DNA Master Application Corrupted