SEA-PHAGES | All posts created by NWCiowaSEAPHAGE

Link to this post \| posted 11 Mar, 2021 17:53
NWCiowaSEAPHAGE	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?

Link to this post | posted 11 Mar, 2021 17:53

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
NWCiowaSEAPHAGE	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
NWCiowaSEAPHAGE	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.

Link to this post | posted 05 Sep, 2019 19:30

NWCiowaSEAPHAGE

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
NWCiowaSEAPHAGE	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
NWCiowaSEAPHAGE	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? Edited 17 Apr, 2019 17:40

Posted in: Cluster AN Annotation Tips → tail assembly chaperone

Link to this post \| posted 18 Jan, 2019 16:47
NWCiowaSEAPHAGE	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? Edited 18 Jan, 2019 19:35

Posted in: Functional Annotation → Membrane protein

Link to this post \| posted 13 Nov, 2018 15:30
NWCiowaSEAPHAGE	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
NWCiowaSEAPHAGE	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
NWCiowaSEAPHAGE	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?

Posted in: Request a new function on the SEA-PHAGES official list → acetyltransferase

Link to this post \| posted 12 Oct, 2017 19:57
NWCiowaSEAPHAGE	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 12 Oct, 2017 19:57

NWCiowaSEAPHAGE

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.

Posted in: tRNAs → tRNA - aa called differently in DNA Master vs. ARAGORN or tRNAscan-SE

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