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Recent Activity
All posts created by debbie
| Link to this post | posted 16 Oct, 2024 13:00 | |
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Excellent! |
Posted in: Arthrobacter → Arthrobacter vanishing plaques
| Link to this post | posted 11 Oct, 2024 14:01 | |
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Terrific! You can do this! debbie |
Posted in: Arthrobacter → Arthrobacter vanishing plaques
| Link to this post | posted 11 Oct, 2024 13:39 | |
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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 |
Posted in: Arthrobacter → Arthrobacter vanishing plaques
| Link to this post | posted 10 Oct, 2024 14:32 | |
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Hi Colleen, Does the control phage provide show no plaques also? debbie |
Posted in: Arthrobacter → Arthrobacter vanishing plaques
| Link to this post | posted 30 Sep, 2024 00:08 | |
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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 |
167KbPosted in: tRNAs → Trimming tRNAs
| Link to this post | posted 17 Jul, 2024 02:20 | |
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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 | |
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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 | |
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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 |
Posted in: Functional Annotation → RefSeq and INSDC name disagreements in NCBI Blast for Functonal Assignment
| Link to this post | posted 18 Jun, 2024 01:34 | |
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Hi Amanda, What do you consider a jumbo phage? thanks, debbie |
Posted in: General Message Board → Jumbo phage annotation
| Link to this post | posted 04 Jun, 2024 01:51 | |
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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 |