Welcome to the forums at seaphages.org. Please feel free to ask any questions related to the SEA-PHAGES program. Any logged-in user may post new topics and reply to existing topics. If you'd like to see a new forum created, please contact us using our form or email us at info@seaphages.org.

Recent Activity

Gordonia singleton annotation help

Link to this post \| posted 20 Feb, 2018 16:10
fogartym1	This semester we are annotating Octobien14 - a Gordonia singleton. When using blastP to help inform our start sites many of the 1:1 alignments that we see are from proteins in bacterial hosts and not bacteriophage. In situations where there is a 1:1 alignment with a bacterial protein and all phage protein alignments are not 1:1, should we just document the bacterial protein alignment, the phage protein alignment, or both?

Link to this post | posted 20 Feb, 2018 16:10

fogartym1

This semester we are annotating Octobien14 - a Gordonia singleton.
When using blastP to help inform our start sites many of the 1:1 alignments that we see are from proteins in bacterial hosts and not bacteriophage. In situations where there is a 1:1 alignment with a bacterial protein and all phage protein alignments are not 1:1, should we just document the bacterial protein alignment, the phage protein alignment, or both?

Link to this post \| posted 21 Feb, 2018 15:47
welkin	You may document the bacterial protein. Singletons are really challenging—just do your best and don't stress over it. I've done singleton annotations that we had to revise once we isolated another five phages from the cluster. Without the comparative genomics, sometimes you just won't know. Good luck! Welkin