Link to this post | posted 30 Sep, 2024 00:08

debbie

Hi Sarah, tRNAs are called by Aragorn 1.1 in DNA Master. The ends were corrected in a later version. The on-line version calls the ends correctly (version 1.2.41) The best set of directions in the Bioinformatics Guide are found here: https://seaphagesbioinformatics.helpdocsonline.com/documenting-trnas You just enter the coordinated in the 3'5'fields of the feature table and copy/paste the product from the on-line version of Aragorn tRNA. I have circled where you enter the coordinates on your power point. debbie 167Kb

Link to this post | posted 17 Jul, 2024 02:20
debbie	A function is now listed on the approved function list with a link to this entry. thank you! debbie

Link to this post | posted 09 Jul, 2024 14:32
debbie	Maria, What gene is your example? I'll add this to the approved function list! debbie

Link to this post | posted 08 Jul, 2024 19:22

debbie

Hi all, Be extremely cautious with using NCBI Blast hits for anything right now. Their Ref_Seq data is at the very least problematic and at its worst is just plain wrong. With our data set being so great, and if you only post 100 hits, using NCBI for anything yields nothing of value over a phagesDB blast because it will only hit our data. If you are not hitting our data, tread just as cautiously because that data may/may not be hand curated. Which means you could be comparing your data to raw Glimmer/GeneMark data with no personal evaluation. So it would not be very helpful. There are many cases in our forums where folks have hit Ref_Seq information that is incorrect. debbie

Link to this post | posted 18 Jun, 2024 01:34
debbie	Hi Amanda, What do you consider a jumbo phage? thanks, debbie

Link to this post | posted 04 Jun, 2024 01:51

debbie

Hi all, GenBank has been re-writing the lineage submission lines for quite a while now. There are 2 issues with what they are doing. First, their records are incomplete. The number of phages that we keep entering is difficult to keep up with, so sometimes they don't offer much. Secondly, we don't really ascribe to this lineage and have found that offering a classification of siphovirus, myovirus, or podovirus may be more helpful. Regardless of what write, they overwrite it. Step carefully as you wade into this to get your MRA published. best, debbie

Link to this post | posted 23 May, 2024 20:28

debbie

Hi Shallee, Rick Pollenz is looking at transmembrane proteins associated with the lysin genes. He may have more insight. Though I am not an expert, it is my understanding that our lysin Bs 'contain' the analogous spanin function of the enteric bacteriophages. So we have avoided using 'spanin' in lieu of lysin B. with the difference in cell walls we would want to be careful that are calls do not cause confusion. You are welcome to deep dive this topic! debbie Edited 23 May, 2024 20:29

Link to this post | posted 21 May, 2024 21:34
debbie	Ping, I can verify that it is down. If it isn't back by tomorrow, i will contact the folks at GeneMark. debbie

Link to this post | posted 15 May, 2024 23:13
debbie	Hi Dane, From the HHPred results, because of the limited nature of the hits, i would not call anything at this time. best, debbie

Link to this post | posted 10 May, 2024 01:15
debbie	Alison and your students, Thank you for your awesome work on this. Maria Gainey presented this and her similar protein at our SMART meeting today and a discussion ensued. For now, we recommend that you call this protein "cyclic nucleotide inhibitor". best, debbie