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Recent Activity
All posts created by debbie
| Link to this post | posted 07 Apr, 2025 18:23 | |
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Thanks so much! Gold star for getting it re-blasted! best, debbie |
Posted in: DNA Master → Blast error
| Link to this post | posted 07 Apr, 2025 16:57 | |
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Randy, Is this so you can submit your genomes for QC? If you can't reBLAST on DNA Master, just record that on your annotation sheet and submit. best, debbie |
Posted in: DNA Master → Blast error
| Link to this post | posted 07 Apr, 2025 12:43 | |
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Hi! What are ribosomal proteins doing in phage genomes? https://www.nature.com/articles/s43705-022-00111-w And what accompanying factors could the phages encode? so many questions! Once you find a significant hit, refer to the Approved Function List to see if we have seen it before. Compare your hits to those to glean more information (if possible). If you find a differrent ribosomal protein, request a review by SMART and we can help to figure out what to add to the list. We will follow this paper for naming, https://pubmed.ncbi.nlm.nih.gov/24524803/ At present, we have 2 hit: bL12 and uL24. Good luck! debbie |
Posted in: Annotation → Ribosomal Proteins
| Link to this post | posted 04 Apr, 2025 17:25 | |
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Hi all, updating will no longer work, but it has to be updated. Follow the directions on this forum post: https://seaphages.org/forums/topic/5577/ |
Posted in: DNA Master → DNA Master on M1 Mac
| Link to this post | posted 04 Apr, 2025 17:05 | |
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The server that held DNA Master is down (likely permanently). Please follow Kristen Butela's work-around. https://seaphages.org/forums/topic/5577/ debbie |
Posted in: DNA Master → DNA Master on M1 Mac
| Link to this post | posted 04 Apr, 2025 17:03 | |
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I think the best call is "ASCE ATPase", that is the term when you can't call it a RecA or provide more specificity. But you know you have an ATP-ase domain, yes? Seems to be missing the C terminus domain of a RecA. Is that what you are asking? debbie |
| Link to this post | posted 27 Mar, 2025 17:16 | |
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Fred, Cluster F1 phages are notorious for the 1-4 base overlaps. The reason I like calling the shorter version of the glycosyltransferase is that it is supported by Starterator AND the HHPred doesn't show alignments in the upstream region of PDB glycosyltransferases. Check out the glycosylation paper about Che8. It should provide more information of best call. https://pubmed.ncbi.nlm.nih.gov/37329881/ debbie Remember that no one piece of data tells the story. It is when we put all of the pieces together that we can see best choices. |
Posted in: Choosing Start Sites → Phage DoRead Start at 52714 bp with 8 bp overlap vs start at 52718 with 4 bp overlap?
| Link to this post | posted 26 Mar, 2025 11:34 | |
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Hi all, The GenBank file will need to include Hypothetical Protein or hypothetical protein. NKF will not be accepted. debbie |
Posted in: Functional Annotation → hypothetical or NKF
| Link to this post | posted 24 Mar, 2025 15:21 | |
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Hi Ann, Yes, we can resend and depending on the dates of the MTA, no further paperwork is required. Would you send me an email for this (djs@pitt.edu). Please include your shipping address (and phone number), or confirm that information is on seaphages.org. Best, debbie |
Posted in: Arthrobacter → Arthrobacter vanishing plaques 2025
| Link to this post | posted 13 Mar, 2025 12:15 | |
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Have you looked here? https://blast.ncbi.nlm.nih.gov/doc/blast-help/ There is a glossary of terms included there. Best, debbie |