SEA-PHAGES | Model Cluster C genome

Link to this post \| posted 25 Aug, 2018 21:14
smolloy123	Hi All, Is there a model cluster C genome I could use to guide function calls? I am QCing two cluster C genomes and I am not super familiar with their genomes. It doesn't help that phagesdb is acting super slow and I cannot capitalize on the "phagesdb" button on PECAAN to immediately see how everyone else called a particular gene within a pham. Could someone recommend a cluster C genome annotated by cluster C experts? And Dan, why is phagesdb so slow these days and why isn't GeneMark cooperating. I think I just broke forum rules sneaking that into this message….

Link to this post | posted 25 Aug, 2018 21:14

Hi All,
Is there a model cluster C genome I could use to guide function calls? I am QCing two cluster C genomes and I am not super familiar with their genomes. It doesn't help that phagesdb is acting super slow and I cannot capitalize on the "phagesdb" button on PECAAN to immediately see how everyone else called a particular gene within a pham.

Could someone recommend a cluster C genome annotated by cluster C experts?

And Dan, why is phagesdb so slow these days and why isn't GeneMark cooperating. I think I just broke forum rules sneaking that into this message…. smile

Link to this post \| posted 29 Nov, 2018 17:02
debbie	While there is never going to be one perfect genome, my students and I are using comparative analyses to arrive at some of our best gene calling. We have recently submitted a set of genomes that are close. As we do more, I will add them. Here are the current ones. Bonray, TinyTim, Khaleesi, McWolfish, Morizzled23, Jessibeth14 Note: I made a decision to follow the tRNA calls of an RNA guy here at Pitt (Dr. Craig Peebles). Some of these tRNAs may not make the infernal score cut-offs, but have passed his inspection. Please follow these tRNA calls in your Cluster C1 genomes.

Link to this post | posted 29 Nov, 2018 17:02

debbie

While there is never going to be one perfect genome, my students and I are using comparative analyses to arrive at some of our best gene calling. We have recently submitted a set of genomes that are close. As we do more, I will add them. Here are the current ones.
Bonray, TinyTim, Khaleesi, McWolfish, Morizzled23, Jessibeth14

Note: I made a decision to follow the tRNA calls of an RNA guy here at Pitt (Dr. Craig Peebles). Some of these tRNAs may not make the infernal score cut-offs, but have passed his inspection. Please follow these tRNA calls in your Cluster C1 genomes.

Link to this post \| posted 22 Jan, 2019 01:52
debbie	In the past few months, my students and I have annotated ~60 Cluster C genomes. While not perfect, they are as good as I get get for now. Remember to follow the guide call the tRNAs EXCEPT using a lower infernal score. We used scores as low as 20.

Link to this post \| posted 16 Apr, 2019 18:20
jlee04	Per the Bioinformatics Guide, contractile-tailed phages should have tail tube protein (Rank 1). I cannot locate it in JPickles. It does not appear in the model genomes listed above: Bonray, TinyTim, Khlessi, etc. Are we just haven't looked hard enough? Or, perhaps they aren't in C1 cluster phages?

Link to this post \| posted 16 Apr, 2019 18:43
debbie	i haven't found it either.

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Model Cluster C genome