SEA-PHAGES | New frameshift in an A1 phage?

Link to this post \| posted 11 Jun, 2018 20:29
grosasacosta	For phages in Cluster A, Tail assembly chaperons are the only type of genes accepted to contain frameshifts. However, while annotating Anglerfish (an A1 subcluster phage), gp13 and gp14 appear to be identical to the N- and C-terminal half regions of capsid maturation protease, respectively. I have searched for slippery sequences and have not found perfect matches, although did find the GGGAGA sequence (very similar to GGGAAA) in the overlapping region. What should be done about this? A BLASTN analysis of this region shows a one-nucleotide difference with Dreamboat on the sequence GGGCGC (this sequence reads GGGCTC in Dreamboat), and this difference is also within the region where the two sequences overlap.

Link to this post | posted 11 Jun, 2018 20:29

For phages in Cluster A, Tail assembly chaperons are the only type of genes accepted to contain frameshifts. However, while annotating Anglerfish (an A1 subcluster phage), gp13 and gp14 appear to be identical to the N- and C-terminal half regions of capsid maturation protease, respectively. I have searched for slippery sequences and have not found perfect matches, although did find the GGGAGA sequence (very similar to GGGAAA) in the overlapping region. What should be done about this? A BLASTN analysis of this region shows a one-nucleotide difference with Dreamboat on the sequence GGGCGC (this sequence reads GGGCTC in Dreamboat), and this difference is also within the region where the two sequences overlap.

Link to this post \| posted 11 Jun, 2018 21:40
welkin	We have no wet bench data for any frameshifts in anything other than the tail assembly chaperones. So while this is cool, we are not going to annotation this with a frameshift between the two pieces.

Link to this post \| posted 12 Jun, 2018 02:04
grosasacosta	Welkin Pope We have no wet bench data for any frameshifts in anything other than the tail assembly chaperones. So while this is cool, we are not going to annotation this with a frameshift between the two pieces. Totally understandable, Welkin. So, should I assign the same function to both genes?

Link to this post \| posted 12 Jun, 2018 12:59
DanRussell	Hey Germán, Since this one was sequenced a while ago, I think I should probably check the sequence in this region to see if it's a sequencing error. I'll get to that ASAP. –Dan

Link to this post \| posted 12 Jun, 2018 14:32
grosasacosta	Sounds good, Dan. Please let me know as soon as you get to it. THANKS!!!

Link to this post \| posted 26 Jun, 2018 20:18
DanRussell	Hey Germán, I was able to find the original data for Anglerfish on one of our old machines. Turns out it is indeed a sequencing error. About 50% of the reads had 4 Cs instead of 3 Cs there, but the consensus was called with 3 Cs. Since it was sequenced in the early days of Ion Torrent, we weren't as good at picking up those errors, but after that definitely confirmed that in cases like that, the longer string was correct. I've added a fourth C to that position in the PhagesDB fasta file. I'll be in touch via email about how to move your existing annotation info to the new sequence. –Dan

Link to this post | posted 26 Jun, 2018 20:18

DanRussell

Hey Germán,

I was able to find the original data for Anglerfish on one of our old machines. Turns out it is indeed a sequencing error. About 50% of the reads had 4 Cs instead of 3 Cs there, but the consensus was called with 3 Cs. Since it was sequenced in the early days of Ion Torrent, we weren't as good at picking up those errors, but after that definitely confirmed that in cases like that, the longer string was correct.

I've added a fourth C to that position in the PhagesDB fasta file. I'll be in touch via email about how to move your existing annotation info to the new sequence.

–Dan

Link to this post \| posted 26 Jun, 2018 21:14
debbie	Germán, Excellent obse4rvaton of the data! -debbie

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New frameshift in an A1 phage?