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All posts created by welkin

| posted 01 Mar, 2018 17:44
We only recently found the slippery site in the Cluster E tail assembly chaperone genes. This means that there are many Cluster E phages in which the frameshift has not been added to the annotation. Make sure you find a Cluster E phage with the frameshift, as all E annotations from now on must have one.
Posted in: Cluster E Annotation TipsTail assembly chaperones?
| posted 01 Mar, 2018 17:19
Gene 1 of Cluster B phages starts on bp1, because we cut the genome to do so.
Posted in: Cluster B Annotation TipsGene 1 start
| posted 01 Mar, 2018 17:08
Thanks to some very successful mass-spectrometry experiments, we know exactly where a number of genes start in the phage Patience. These experiments are reported in mBio, along with a table of the genes that we've identified starts for. You should use the equivalent start positions for all Cluster U annotations.
Posted in: Cluster U Annotation TipsGene Starts in Cluster U
| posted 01 Mar, 2018 17:03
Lucky annotators of Cluster B phages are off the hook for adding frameshifts to their annotations, as we have not yet been able to identify which genes are the tail assembly chaperones in Cluster B.
Posted in: Cluster B Annotation TipsTail assembly chaperones?
| posted 01 Mar, 2018 15:40

Cluster B phages do not have a separate capsid maturation protease and scaffolding protein. instead, they have a great big long protein called a capsid morphogenesis protein. a capsid maturation protease and MuF-like fusion protein.
Edited 16 Mar, 2021 18:29
Posted in: Cluster B Annotation TipsCapsid maturation protease and MuF-like fusion protein
| posted 01 Mar, 2018 15:39
The portal functional assignment was mistakenly added to a number of old Cluster B phages in our database. Make sure that you have one and only one portal in your annotation, and that you've chosen the gene that has an HHpred match to a portal crystal structure.
Posted in: Cluster B Annotation TipsPortals
| posted 01 Mar, 2018 15:37
Unlike many other phages, the immunity repressor is not located adjacent to the integrase or partitioning genes in the Cluster A phages. Instead, it is far over in the right arm (around genes 68-70 or so).
The immunity repressor's start has been confirmed at the bench, and should use the same start as L5 and Bxb1. There is a large space in the coding genes upstream of the start of the gene, this is because there is a promoter and an operator sequence in the gap. Do not make your immunity repressor too long!
Posted in: Cluster A Annotation Tipsthe immunity repressor
| posted 01 Mar, 2018 15:32
Cluster A phages have some of the most wet bench support for the confirmation of starts of their genes.
This includes the integrases. Serine integrases should use the same start as Bxb1, while tyrosine integrases should use the same start as L5.
Posted in: Cluster A Annotation Tipsthe start of the integrase
| posted 01 Mar, 2018 15:30
Gene 1 in Cluster A phages is usually a HNH endonuclease oriented in the forwards direction. Cluster A4 phages in particular sometimes fool the gene prediction programs and put a small gene in the reverse orientation as gene 1. Don't be fooled! The reverse gene is a false prediction and should be deleted. You will likely have to manually add the real one.
Posted in: Cluster A Annotation TipsGene 1
| posted 21 Feb, 2018 16:44
Hi Joann,
Did you remember to change the number of regions in the description tab to "2" ?

Posted in: Frameshifts and IntronsAnnotation advise: Frameshift in A4