Link to this post | posted 20 Dec, 2024 03:42

debbie

Christine, With no experimental evidence, it is difficult to say which it is, but it is thought that the +1 frameshift is far more common than the -2. So that is what I would annotate. There are a lot of unannotated frameshifts in this subcluster, mostly becsuse we made a decision to only annotate those sequences found in the literature. (See the guide for the list). However, this sequence is so well conserved, i think it can be called. debbie

Link to this post | posted 16 Oct, 2024 13:00
debbie	Excellent!

Link to this post | posted 11 Oct, 2024 14:01
debbie	Terrific! You can do this! debbie

Link to this post | posted 11 Oct, 2024 13:39
debbie	Hi Colleen, The simplest answer is that you are not propagating A. globi any longer. Do you have your original stock material? It is time to revert to that! A good practice is that all cultures be subbed from the parental strain, an F1 or F2 generation is fine, but going beyond that is problematic. Best, debbie

Link to this post | posted 10 Oct, 2024 14:32
debbie	Hi Colleen, Does the control phage provide show no plaques also? debbie

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