SEA-PHAGES | TAC Frameshift in BJ and BN

TAC Frameshift in BJ and BN

Link to this post \| posted yesterday, 19:43
lhughes	The following sequence is called as the slippery sequence in the cluster BJ phage Dubu (GGGAAAC, in Dubu_13), which matches the XXXYYYZ pattern that has been called elsewhere (example is the BK1 phage as discussed here: https://seaphages.org/forums/topic/5168/?page=1). BN phages have a TAC in the same pham as the TAC of Dubu (CF phage also have this pham, but only one has the frameshift called, Jflix2_18 which has GGGTTTC. None of the other CF phage have the XXXYYYZ at that location). The frameshift has not been previously called in this cluster, but all 10 members of the cluster contain this pham (two genes upstream of the tapemeasure) and the GGGAAAC is conserved in all of them. I am QCing Greenbelt, which my students just annotated, and they chose to call this frameshift. I believe that they are correct and plan to include this in the final file. Assuming there is nothing I am missing, I also plan to add a note in the cluster-specific forum page for BN (as well as BJ, which doesn't currently have a TAC note) to provide information about looking for this frameshift. How does this sound to everyone? Let me know if you need more information. Lee

Link to this post | posted yesterday, 19:43

The following sequence is called as the slippery sequence in the cluster BJ phage Dubu (GGGAAAC, in Dubu_13), which matches the XXXYYYZ pattern that has been called elsewhere (example is the BK1 phage as discussed here: https://seaphages.org/forums/topic/5168/?page=1).

BN phages have a TAC in the same pham as the TAC of Dubu (CF phage also have this pham, but only one has the frameshift called, Jflix2_18 which has GGGTTTC. None of the other CF phage have the XXXYYYZ at that location). The frameshift has not been previously called in this cluster, but all 10 members of the cluster contain this pham (two genes upstream of the tapemeasure) and the GGGAAAC is conserved in all of them. I am QCing Greenbelt, which my students just annotated, and they chose to call this frameshift. I believe that they are correct and plan to include this in the final file.

Assuming there is nothing I am missing, I also plan to add a note in the cluster-specific forum page for BN (as well as BJ, which doesn't currently have a TAC note) to provide information about looking for this frameshift.

How does this sound to everyone? Let me know if you need more information.

Lee

Link to this post \| posted today, 01:42
debbie	Lee, It sounds correct to me! XXXYYYZ is always a winner! debbie

Recent Activity

TAC Frameshift in BJ and BN