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Recent Activity
All posts created by NWCiowaSEAPHAGE
| 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? |
Posted in: Request a new function on the SEA-PHAGES official list → Zinc finger DNA binding domain/protein
| Link to this post | posted 19 Oct, 2017 19:26 | |
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We also have many BLAST hits for an N-acetyl transferase on PhagesDB BLAST and NCBI BLAST. When I tried HHPred I got many hits for acetyl transferases (around a probability of 90). Is this a function we can use? |
| Link to this post | posted 12 Oct, 2017 19:57 | |
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We have a tRNA gene in a tRNA cluster within our C1 phage, Roots515, that DNA Master says is for serine but ARAGORN and tRNAscan-SE say is for leucine. Additionally, the anticodon is almost always consistent between ARAGORN and tRNAscan-SE but different in DNA Master. This is our first experience annotating tRNAs but, as you can imagine, we have many to do for our C1 phage! Any advice is most welcome! Thanks. |
| Link to this post | posted 22 Sep, 2017 19:24 | |
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Problem solved! Thank you so very much!! |