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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 01 Mar, 2021 00:52 | |
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The pfam hits to holin are not great but also not shabby. The typical order of genes is not present in the B1s, so that is also not helpful. However, it is interesting that this gene has 4 transmembrane domains, and the 2 subsequent genes each have 2 transmembrane domains. So I would be inclined to call all three "membrane proteins". |
Posted in: Cluster B Annotation Tips → Holin
| Link to this post | posted 26 Feb, 2021 19:51 | |
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Hi Shallee, What genes are you referring to? thanks, debbie |
Posted in: Cluster B Annotation Tips → Holin
| Link to this post | posted 26 Feb, 2021 13:12 | |
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Hi! I am not sure the evidence is convincing. I would like to investigate a bit. |
Posted in: Functional Annotation → riiA and riiB like proteins
| Link to this post | posted 20 Feb, 2021 00:04 | |
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You're welcome! |
Posted in: Functional Annotation → PLA2-like domain in Cluster B1s
| Link to this post | posted 19 Feb, 2021 23:49 | |
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I do not think that this protein (gene35 of Sarma624) has a reportable function. HHPred has no hits to an applicable function. |
Posted in: Functional Annotation → PLA2-like domain in Cluster B1s
| Link to this post | posted 19 Feb, 2021 01:09 | |
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Yep. Looks like an error to me. We will get this corrected as we continue with genome curations. Thanks! debbie |
| Link to this post | posted 15 Feb, 2021 17:07 | |
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Joe, It doesn't matter, just state (maybe in your cover letter) what you used. debbie |
Posted in: Annotation → % alignment
| Link to this post | posted 09 Feb, 2021 23:26 | |
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Hi Greg, The jury is really out on all of this. We are in need of wet bench data, which is coming, but not here yet. There is just no answer at this time. I ran a comparison of the different settings and the new setting will work for now. An alternative when you run with the old settings is to parse the sequence into parts. I ran a 20kb length of a bigger genome and was able to run it at the previous setting easily. All i have for right now. Will update with additional data. a;ways check the Bioinformatics Guide for latest settings because I will keep it updated. Thanks, debbie |
Posted in: tRNAs → tRNAScan-SE Down-ish?
| Link to this post | posted 06 Feb, 2021 19:05 | |
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Hi all, The site is not broken. It just won't run in any timley fashion with the settings we have been using. We did some fiddling with our settings and have modified how to run tRNA Scan SE. Go to the Bioinformatics Guide to get them! |
Posted in: tRNAs → tRNAScan-SE Down-ish?
| Link to this post | posted 06 Feb, 2021 18:54 | |
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and I just revised the protocol again. |
Posted in: tRNAs → tRNAscan-SE site has changed?