SEA-PHAGES | Auto-annotation fix for fall 2017 and later

Link to this post \| posted 04 Dec, 2017 16:22
DanRussell	In 2017, NCBI decided to no longer host public instances of GeneMark and Glimmer, which were used by DNA Master to perform auto-annotations. If your copy of DNA Master is failing to auto-annotate, see the post below about how to get it working again. https://seaphages.org/blog/2017/10/27/auto-annotation-fix-dna-master/ –Dan

Link to this post \| posted 12 Jan, 2018 19:52
RuchiraS	Hey Dan, I tried this but my DNAMaster is only predicting tRNAs. This link did work before but its not working now. Thanks

Link to this post \| posted 17 Jan, 2018 17:56
DanRussell	I think perhaps our servers were just down around Jan 12. Is it working now? –Dan

Link to this post \| posted 24 Jan, 2018 19:59
ptsourkas	Still not working for me, as of January 24 2018. I get "Glimmer failure" and "Annotation failure". Thanks, Philippos

Link to this post \| posted 26 Jan, 2018 16:38
GregFrederick@letu.edu	We are getting a lot of skipped genes of autoannotated genes. We can go in and blast them individually but most still fail. We can ad do use BlastP on phagesDB but then the documentation is not in the Blast section of DNA Master and it is difficult to confirm that students have actually done this analysis. I do not think I ever saw these skipped Blasts on previous genomes. But I have not done as many as many of you. Thoughts? Is it a server problem, something with our genome annotation or something else? Thanks. greg

Link to this post | posted 26 Jan, 2018 16:38

GregFrederick@letu.edu

We are getting a lot of skipped genes of autoannotated genes. We can go in and blast them individually but most still fail.

We can ad do use BlastP on phagesDB but then the documentation is not in the Blast section of DNA Master and it is difficult to confirm that students have actually done this analysis.

I do not think I ever saw these skipped Blasts on previous genomes. But I have not done as many as many of you.

Thoughts? Is it a server problem, something with our genome annotation or something else?

Thanks. greg

Link to this post \| posted 26 Jan, 2018 20:46
DanRussell	ptsourkas Still not working for me, as of January 24 2018. I get "Glimmer failure" and "Annotation failure". Thanks, Philippos Hi Philippos, Is your DNA Master up to date? If you run Update does all look good? Any other weird errors popping up? I think the servers are working. You've entered the proper access code in the linked document? –Dan

Link to this post \| posted 26 Jan, 2018 20:48
DanRussell	GregFrederick@letu.edu We are getting a lot of skipped genes of autoannotated genes. We can go in and blast them individually but most still fail. We can ad do use BlastP on phagesDB but then the documentation is not in the Blast section of DNA Master and it is difficult to confirm that students have actually done this analysis. I do not think I ever saw these skipped Blasts on previous genomes. But I have not done as many as many of you. Thoughts? Is it a server problem, something with our genome annotation or something else? Thanks. greg Hi Greg, To be clear: your problem is with BLAST, not auto annotation itself? Meaning you get all the features, but only some of them have BLAST results? BLASTing all genes can sometimes end up with genes being skipped, especially if done during peak hours. What phage are you working on? –Dan

Link to this post | posted 26 Jan, 2018 20:48

DanRussell

GregFrederick@letu.edu
We are getting a lot of skipped genes of autoannotated genes. We can go in and blast them individually but most still fail.

We can ad do use BlastP on phagesDB but then the documentation is not in the Blast section of DNA Master and it is difficult to confirm that students have actually done this analysis.

I do not think I ever saw these skipped Blasts on previous genomes. But I have not done as many as many of you.

Thoughts? Is it a server problem, something with our genome annotation or something else?

Thanks. greg

Hi Greg,

To be clear: your problem is with BLAST, not auto annotation itself? Meaning you get all the features, but only some of them have BLAST results?

BLASTing all genes can sometimes end up with genes being skipped, especially if done during peak hours. What phage are you working on?

–Dan

Link to this post \| posted 26 Jan, 2018 22:47
GregFrederick@letu.edu	Hi Dan. There are a few gaps in the auto-annotation results that we will likely need to adjust. But we expected that based on previous genomes. The "Blast All Genes" function in DNA Master worked completely on 2 of four genomes we are working on. On the other two, 10-20% of the auto-annotated genes appear to simply have been skipped by the process. I don't know what time the students ran their blasts But your explanation is helpful. Thanks. Greg

Link to this post | posted 26 Jan, 2018 22:47

GregFrederick@letu.edu

Hi Dan.

There are a few gaps in the auto-annotation results that we will likely need to adjust. But we expected that based on previous genomes.

The "Blast All Genes" function in DNA Master worked completely on 2 of four genomes we are working on. On the other two, 10-20% of the auto-annotated genes appear to simply have been skipped by the process. I don't know what time the students ran their blasts But your explanation is helpful.

Thanks. Greg

Link to this post \| posted 26 Jan, 2018 22:49
GregFrederick@letu.edu	ptsourkas Still not working for me, as of January 24 2018. I get "Glimmer failure" and "Annotation failure". Thanks, Philippos Some of our students were getting similar errors until we walked through all the new preferences settings. Once I sat with them and confirmed those setting (which takes time for 25 students) things seemed to work correctly.

Link to this post \| posted 20 Feb, 2018 22:15
GregFrederick@letu.edu	RuchiraS Hey Dan, I tried this but my DNAMaster is only predicting tRNAs. This link did work before but its not working now. Thanks We are getting this same result today. It occurred both earlier this AM and again this afternoon. Are the servers down again today????

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Auto-annotation fix for fall 2017 and later