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Recent Activity
byrumc@cofc.edu posted in Getting Started with Phage Assembly
byrumc@cofc.edu posted in Getting Started with Phage Assembly
byrumc@cofc.edu posted in Getting Started with Phage Assembly
byrumc@cofc.edu posted in Classificiation with ICTV guidelines
Debbie Jacobs-Sera posted in Classificiation with ICTV guidelines
All posts created by debbie
| Link to this post | posted 24 Jun, 2020 13:54 | |
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In fact, there are no hits to tail assembly chaperones proteins in DH, so for now, we are not going to call them at all. |
Posted in: Cluster DH Annotation Tips → Tail assembly chaperones?
| Link to this post | posted 23 Jun, 2020 23:51 | |
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Let me know how it goes! |
Posted in: DNA Master → TbFeatures error
| Link to this post | posted 23 Jun, 2020 23:29 | |
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Do you a complete set of documentation in one of your files? Copy it from whatever corrupted file it is in and paste it into the (empty) documentation of a perfect sequence file. (To get that sequence file, open a .fasta and stop before you auto-annotate.) Then parse. You won't have blast data, but you also won't have to re-enter as much. You can cut and paste from multiple files. Sorry I can't do better. |
Posted in: DNA Master → TbFeatures error
| Link to this post | posted 23 Jun, 2020 23:18 | |
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Christos, I unpacked one of my files, so how your file was broken is extraordinary. My next advice is to revert to an older file that is not broke or to cut and paste from documentation. let me know if I can help. debbie |
Posted in: DNA Master → TbFeatures error
| Link to this post | posted 23 Jun, 2020 14:55 | |
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Christos, I am still unsuccessful, but checking. Can you open and use a different .dnam5 file on your machine? Was PECAAN used to create your file? What is the next best version of your file? debbie |
Posted in: DNA Master → TbFeatures error
| Link to this post | posted 18 Jun, 2020 12:51 | |
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Ok. Could you send me the file and let me try? I also couldn't fix a file recently, so I may need to get some help from Dr. Lawrence. Thanks, debbie |
Posted in: DNA Master → TbFeatures error
| Link to this post | posted 12 Jun, 2020 11:21 | |
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Hi Christos, This how you fix the file. It is a bit tedious. https://seaphagesbioinformatics.helpdocsonline.com/article-104 Good luck, debbie |
Posted in: DNA Master → TbFeatures error
| Link to this post | posted 02 Jun, 2020 17:03 | |
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JoAnn, I agree. The top hit is to HK97 gp 10. This phage is well studied by the Hendrix lab here at Pitt and while this is a structural protein in that phage, its function is unknown. The second hit is to a minor capsid protein. So it is easy to assume that this is a structural gene, which one is unknown. debbie |
| Link to this post | posted 30 May, 2020 15:52 | |
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As you do a final check of your genomes, please review/compare the functions exported from PECAAN with the approved Functions List. Updates for both of these lists is a manual action, and not entirely synchronous. |
Posted in: PECAAN → Approved Functions in PECAAN
| Link to this post | posted 30 May, 2020 15:50 | |
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Sigma factors and transcription factors are gene assignments that are use across all organisms. Gene regulation is everywhere! They are not unique to prokaryotes, and as such, they have diverse means in the context of, at the very least, prokaryotes vs eukaryotes. Today, May 30, 2020, we are going to avoid them all together and call such hits "DNA binding proteins" for now. One of the exceptions is WhiB. We will still call "WhiB family transcription factor" when appropriate. debbie |
Posted in: Annotation → sigma factors & transcription factors