Link to this post | posted 22 Oct, 2020 01:06
debbie	Thanks Chris!

Link to this post | posted 21 Oct, 2020 19:12

debbie

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 76Kb

Link to this post | posted 09 Oct, 2020 17:20
debbie	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

debbie

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!

Link to this post | posted 26 Sep, 2020 19:37
debbie	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

Link to this post | posted 24 Sep, 2020 11:46
debbie	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

Link to this post | posted 20 Sep, 2020 19:16
debbie	We have more experimental data for -1 frameshifts. So we will call the -1 until we can do an experiment to differentiate. debbie

Link to this post | posted 11 Sep, 2020 20:53
debbie	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

Link to this post | posted 09 Sep, 2020 01:45
debbie	Steve, Check the build, I think that he has not updated DNA Master. debbie

Link to this post | posted 08 Sep, 2020 19:52

debbie

Jasmin, HI. There are 2 common errors that can cause this. One is that our permission to use the Glimmer server ran out and needs to be updated. I have ruled that out because I was able to auto-annotate and obtain Glimmer results. The second reason is usually that the settings are incorrect in Preferences. Have them check # 2 at this page of the guide. The unlock code is Hatfull; there is no password. https://seaphagesbioinformatics.helpdocsonline.com/article-66