Link to this post | posted 15 Mar, 2022 13:16
debbie	Shima, What you need to provide is one best explanation for each gene call. Since i don't use PECAAN this way, I can't answer your question. You are correct, Claire set up PECAAN so there is an output that works. But whatever you pick, be sure to identify the problem areas and the thinking process. debbie

Link to this post | posted 15 Mar, 2022 13:03
debbie	There is another string of forum posts in the cluster specific annotation tips. I just looked at a set of these genes (see the post) and I am worried that the wrong genes are being implicated. Use your phage's HHpred data to make your decisions. https://seaphages.org/forums/topic/5009/ Best, debbie

Link to this post | posted 07 Mar, 2022 20:56

debbie

Hi Vicky, Here is my 2 cents. I don't think that gene 21 and 22 are tail assembly chaperones. Using the HHPred info in PECAAN. Gene 21 (16902 - 1722 hits the MuF-like protein that we don't quite understand and are currently calling it a Hypothetical Protein. Gene 22 (17225 - 17635) Significantly hits minor capsid genes, and tail genes. In particular it hits HK07-gp10. That phage was well studied at Pitt and those researchers did not know the function of gp10, so it too is a hypothetical protein, Gene 23 (17682-18221) DOES have a significant hit to a tail assembly chaperone (pfam hit). BUT it is in the right place, so I would consider it. This is my first pass on this. If you read the Cluster specific annotation tip on this subject, you can see others have struggled with this also. https://seaphages.org/forums/topic/5009/ Next step, please run all HHpred at HHPred. IGNORE ALL PREVIOUS SEA-PHAGES ANNOTATIONS. When this first of this Cluster (CloverMinnie and Sour) we thought the TAC HAD TO BE THERE. We now know that is not true. As you re-evaluate this, let me know if you need additional help. Good luck! debbie

Link to this post | posted 02 Mar, 2022 20:47

debbie

The paper about the queuosine pathway found in Rosebush was published in 2019. I was hoping to have curated those phams and gotten it recorded in phamerator in a better way, but that curation is lagging further behind the data than hoped for. The paper contains the empirical bench data that we want to capture in our annotation. So while others could interpret bioinformatic hits diferently, Rosebush genes have empirical bench data to support the calls. Once the paper was published, Dr. Hatfull and I carefully chose the names to call the genes. They are recorded in the case study that I mentioned. A few minutes ago, I sat down with Christian and he updated the annotation of Rosebush in phamerator for the gene names of the first 6 genes. The processing will take a bit of time, and then the data will have to be transferred to the web version. BUT, in a few hours Rosebush will reflect the correct gene functions for these genes. In the meantime, follow the "Gene assignment as per approved function list" in the table about Rosebush in the aforementioned case study. Sorry for the confusion. debbie

Link to this post | posted 02 Mar, 2022 18:56
debbie	Hi Erin, Did you check out the case study in the Bioinformatics Guide? https://seaphagesbioinformatics.helpdocsonline.com/article-1596481355 I can't quite answer a general question, but if you give me the specifics, I can try to help. Thanks, debbie

Link to this post | posted 01 Mar, 2022 17:40
debbie	And the second thing to so do is to make sure you are running as Adminisitrator when you update. best, debbie

Link to this post | posted 18 Feb, 2022 17:58
debbie	Hi Amaya, did the students do this: https://seaphagesbioinformatics.helpdocsonline.com/article-104 Sounds like they corrupted their file. debbie

Link to this post | posted 16 Feb, 2022 18:50
debbie	Sounds like a great student project!

Link to this post | posted 15 Feb, 2022 20:11
debbie	yep!

Link to this post | posted 15 Feb, 2022 18:22

debbie

Hi all, Sally Molloy also weighed in: I attached a paper describing prokaryotic Hfq proteins (see figure 2). I think the protein actually has the conserved residues required for the two Sm domains of an Hfq protein including: 1) it has the conserved G in Beta2 that is found in all Sm proteins 2)It has the highly conserved hydrophobic residues characteristic of the first Sm domain 3) It has the highly conserved G of Sm1 but is missing the second highly conserved D of Sm1. 4) It has the absolutely conserved Q of alpha helix 1 and it has the highly conserved Y/F in Sm1 It is missing the YKH motif of the SM2 motif but instead has an HRS motif (the eukaryotic motif here is simply RG). So its pretty similar in terms of secondary structure and conserved amino acids to Gram positive Hfq proteins. I think we can at least call it an RNA binding protein and maybe an Hfq protein. Cheers, Sally Molloy I personally am inclined to call these proteins "RNA binding proteins". debbie 833Kb