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Recent Activity
All posts created by NWCiowaSEAPHAGE
| Link to this post | posted 16 Mar, 2021 14:07 | |
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I don't think capsid morphogenesis protein is on the approved functions list. Could someone add it please? Thanks! |
| Link to this post | posted 12 Mar, 2021 18:49 | |
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Thanks Chris! I will definitely work through that paper with my students. |
Posted in: Annotation → Membrane proteins
| Link to this post | posted 11 Mar, 2021 17:53 | |
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My students love calling membrane proteins this semester for some reason. What do I advise them to do with proteins that have two or more good TM domains (using at least 2 different programs) but no phagesdb BLAST membrane protein calls. So far, I've been explaining that hydrophobic helices can be internal to proteins as well as serve as TM domains. I've told them they need more evidence than 2 or more good TM domains predicted to make a membrane protein call. Am I giving them good advice or should I be more liberal in calling membrane protein? |
Posted in: Annotation → Membrane proteins
| Link to this post | posted 26 Feb, 2020 17:58 | |
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Are there any videos that walk someone through figuring out genome ends (using PAUSE)? |
Posted in: Annotation → Assembly
| Link to this post | posted 05 Sep, 2019 19:30 | |
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We are annotating a B Cluster phage with no subcluster. We have a reverse gene whose start site we'd like to call (to capture all CP) doesn't leave room for a promoter even though it is a reverse gene in a sea of forwards (it is a ~25 bp overlap). Other similar phages also leave no room for a promoter in this region of the genome. I'd love to get some of your thoughts on calling a start to include all CP but leave no room for a change of direction promoter. |
Posted in: Annotation → space for a promoter when changing direction?
| Link to this post | posted 19 Apr, 2019 18:28 | |
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Debbie–just to be really clear–the peak of coding potential just upstream of tape measure protein in Blair and the phage we are working on, Laila, called by neither GeneMark nor Glimmer (peaking right around 7200) is probably not a gene? Thanks! - Sara |
Posted in: Cluster AN Annotation Tips → Recheck of the genes between major capsid and tape measure gene
| Link to this post | posted 17 Apr, 2019 17:38 | |
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Are we annotating a frameshift for this cluster or waiting for more evidence? I'm assuming no for now since none of the ANs have annotated a frameshift? |
Posted in: Cluster AN Annotation Tips → tail assembly chaperone
| Link to this post | posted 18 Jan, 2019 16:47 | |
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Does a gene that BLASTs to Membrane protein, Band-7-like need to have multiple transmembrane domains to call it Membrane protein, Band-7-like? |
Posted in: Functional Annotation → Membrane protein
| Link to this post | posted 13 Nov, 2018 15:30 | |
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I don't think adenylate kinase is on the approved functions list yet. Can it be added? |
Posted in: Cluster B Annotation Tips → B1 Gene 1
| Link to this post | posted 19 Oct, 2017 19:36 | |
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We have a gene in our C1 phage with many hits to a zinc-finger DNA binding domain/protein in PhagesDB BLAST and NCBI BLAST. We used HHPred and got several hits to zinc finger proteins with probabilities above 95. Is this a function we can use? |