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All posts created by smg366
| Link to this post | posted 18 Apr, 2024 11:16 | |
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Hi, I am trying to use PhamNexus on the seaphage 2020 VM. When I open it and search for updates to the database it says there are no updates available. When I click through to select files there are no cluster names or phage names or listed for me to select. How can I access the files on the database? Thank you |
Posted in: Bioinformatic Tools and Analyses → PhamNexus on SEA-VM
| Link to this post | posted 22 May, 2023 13:41 | |
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What are we calling the gene in the B cluster with pfam hits to holin, discussed above?. Phage Inverness gp16 has 95% probability with 40% coverage to holin on HHPRED. HHPRED results in the attachment. There are still only 13 B cluster phages calling holin and the rest calling Hypothetical protein. |
157KbPosted in: Cluster B Annotation Tips → Holin
| Link to this post | posted 10 Apr, 2023 07:19 | |
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I am a little confused with our current calling of membrane proteins. Should we be calling membrane proteins as functions within our annotations? From PhagesDB and Phamerator it looks like there is a move away from that. |
Posted in: Annotation → Membrane proteins
| Link to this post | posted 10 Apr, 2023 07:19 | |
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I am a little confused with our current calling of membrane proteins. Should we be calling membrane proteins as functions within our annotations? From PhagesDB and Phamerator it looks like there is a move away from that. |
Posted in: Annotation → Membrane proteins
| Link to this post | posted 20 May, 2022 14:07 | |
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Thank you for getting back to me so quickly! Susan |
Posted in: Functional Annotation → Membrane protein
| Link to this post | posted 20 May, 2022 14:02 | |
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I am doing QC for a DE genome, where there are a number of Membrane Protein functions called. SOSUI, TMHMM and Topcons all support at least 2 transmembrane domains, but no other phages have called membrane proteins for these genes. I just want to check that we are still calling membrane protein as a function if there is evidence for it? |
Posted in: Functional Annotation → Membrane protein
| Link to this post | posted 14 Dec, 2021 10:15 | |
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Hi Debbie, Running as an administrator has allowed me to open my file and the RBS information is now visible. Thank you, Susan |
Posted in: DNA Master → TbQueries
| Link to this post | posted 13 Dec, 2021 17:16 | |
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My student and I are having a similar error. We both downloaded DNA Master, ran as administrator to update DNA Master, but now on trying to open an Archived file get the error message "TbQueries: Cannot perform this operation on a closed dataset". I have tried to open multiple files and keeping getting the same error. Before running the update to DNA Master, the files were running, but without the gene numbers in Frames, and without RBS Z-score and final score. What should we do next to allow us to open the file? Thanks, Susan |
Posted in: DNA Master → TbQueries
| Link to this post | posted 25 Jul, 2021 15:52 | |
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Hi, I am trying to generate a flat file and submission file for phage Colbster. The files looks fine in DNA Master, but after entering the Genbank Submission information I can't "process" the file. It generates a GBS file and says "Save GBS before closing?", in the Events tab the error says "Error flushing table". I was able to generate files for my other 4 genomes and I tried turning everything off then on again. How can I fix this error to generate the files? Thanks, Susan |
Posted in: DNA Master → Error flushing tables
| Link to this post | posted 08 Jun, 2021 10:27 | |
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Drexel University is looking to hire an Assistant Teaching Professor which will including teaching SEA-PHAGES and SEA-GENES courses. Drexel currently runs 4 sections of SEA-PHAGES (92 students) and 1 section of SEA-GENES (24 students). The goal is to hire for the start of the Fall quarter in September 2021. More information can be found at the link below: https://careers.drexel.edu/en-us/job/495969/assistant-teaching-professor |