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 06 Oct, 2020 20:17 | |
|---|---|
|
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 | |
|---|---|
|
|
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 | |
|---|---|
|
|
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 | |
|---|---|
|
|
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 | |
|---|---|
|
|
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
| Link to this post | posted 09 Sep, 2020 01:45 | |
|---|---|
|
|
Steve, Check the build, I think that he has not updated DNA Master. debbie |
Posted in: DNA Master → Novel Student Issue
| Link to this post | posted 08 Sep, 2020 19:52 | |
|---|---|
|
|
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 |
Posted in: DNA Master → Glimmer Failure on Auto Annotation
| Link to this post | posted 05 Sep, 2020 13:16 | |
|---|---|
|
|
An update to DNA Master has been posted. Blast will not work unless you update. The latest version is Version 5.23.3 Build 2657 4Sep2020 |
Posted in: DNA Master → Blast error
| Link to this post | posted 04 Sep, 2020 19:46 | |
|---|---|
|
|
Kyle, It is up to GenBank. They promise an accession number in 3 days when a genome is submitted. Then they have to process it. That time is unpredictable. My last submissions took ~ month. debbie |
Posted in: Annotation → In Genbank
| Link to this post | posted 04 Sep, 2020 14:15 | |
|---|---|
|
|
No worries. Par for the course. |
Posted in: DNA Master → Blast error