Link to this post | posted 13 Feb, 2018 16:43

GregFrederick@letu.edu

Our analysis process (tell me if we can save time anyway or streamline the process): 1. If, via the DNA Master Internal NCBI BlastP analysis, we ID a definite defined (according to the current approved function list), we list this function under SIF-Blast. 2. If the automated NCBI Blast inside DNA Master Blast only lists "theoretical protein" or proteins of NKF, we blast the product in PhagesDB and individually on the NCBI BlastP website to examine lower ranked hits for potential function. 3. If the Blast analyses in #1 and #2 do not lead us to a function, we step to HHPred analysis. If we see an HHPred defined function with an E value of better than e-16 or >90% probability across the majority of the protein we are recording it under SIF-HHPred. 4. If we do not find a function via steps #1 though #3 above, we look for a function via synteny. QUESTIONS: A. If we ID an allowed function via Blast analysis, it seems unnecessary to do the HHPred analysis. Do we really need to record the SIF HHPred results for those features where BlastP IDs are 100%? B. If the condition in Question A above is met, do we actually need to record the SIF-Syn info from Phamerator in the notes for DNA Master? We are annotating a lot of phages this semester, with very few students and I don't think we will get some of them fully annotated if these seemingly redundant data points must be included for every feature. Help?!?! Edited 13 Feb, 2018 16:46

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 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 17:37
GregFrederick@letu.edu	Is the notes template in PECAAN updated with to add the new (2018 Annotation Guide) notes template? Specifically the 3 SIF: notes, RBS: instead of SD: and others? "I want to know for sure…" Thanks. GF

Link to this post | posted 26 Jan, 2018 17:13
GregFrederick@letu.edu	Related Question: Related to the SIF: notation in the Bioinformatics Guide QUESTION: Am I correct that if we get a solid function ID from the BlastP analysis that the HHPred analysis is unnecessary? Same for SIF: Synteny? (Trying to save the QC team a lot of editing and possibly myself if we do the 400 features we are annotating this semester incorrectly.) Edited 26 Jan, 2018 17:14

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 25 Jan, 2018 23:01

GregFrederick@letu.edu

We are experiencing a very long lag in loading the Starterator analysis page through the PhagesDB website. http://phagesdb.org/phams/ Is anyone else experiencing this? I'm wondering if it is our bandwidth or a phagesdb.org bandwidth problem. Is it possible we are overloading the phagesDB server with requests. Some of the student computer lab computers are taking 60-80 seconds just to load the http://phagesdb.org/phams/ where the pham numbers are input. Thoughts? Are you experiencing page load lags? Thanks. Greg

Link to this post | posted 10 Jan, 2018 19:38
GregFrederick@letu.edu	When students follow the DNA Master Quick Start Guide they are getting a Glimmer Fail message and the auto-annotate process fails to complete. I tried to run the same fasta file on my notebook and I did not get the Glimmer fail error message. But the process just aborts. What am I missing? Is something different this year? Thanks for any advise. Greg

Link to this post | posted 20 Mar, 2017 17:58
GregFrederick@letu.edu	Thanks Welkin! I'll let the students know. GF

Link to this post | posted 15 Mar, 2017 22:36
GregFrederick@letu.edu	Thanks Welkin. We will delete the tRNA. It really seems real. So is there any empirical evidence that there are not tRNAs overlapping with structural genes? Since these are in the opposite orientation, if seems feasible that both could be real.