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
Debbie Jacobs-Sera posted in Whole phage starterator reports
cdshaffer posted in Whole phage starterator reports
Shallee Page posted in Plaques appear on spot test, don't appear in titer
Viknesh Sivanathan posted in Plaques appear on spot test, don't appear in titer
Debbie Jacobs-Sera posted in Plaques appear on spot test, don't appear in titer
Cluster G1 Gene Start
| Link to this post | posted 05 Apr, 2022 15:53 | |
|---|---|
|
Hi we have a question concerning the start for a cluster G1 phage, GoldenAsh_1: • Glimmer calls the start at 46; GeneMark at 43. Hard to see exactly where the coding potential begins on the GeneMarkS readout. • The Starterator report does not show consensus; the most called start is at bp 43, but only in 33/93 annotated genomes. • BLASTP shows alignment from the beginning of the protein with phages containing 113 amino acids; some phages have 114 amino acids, however. Likely function: terminase, small subunit. • HHPred has a slightly higher probability with the shorter protein starting at bp 43 (92% vs. 90%). The evidence doesn’t show clear support for the longer ORF/protein, so we were going to stick with the original Glimmer call at bp 46. Any thoughts would be appreciated! I attached the annotation template with screenshots. |
3.25Mb| Link to this post | posted 05 Apr, 2022 19:28 | |
|---|---|
|
This forum post may be useful https://seaphages.org/forums/topic/4347/ Cheers |
| Link to this post | posted 05 Apr, 2022 20:01 | |
|---|---|
|
|
Hi Veronique, Thank you very much for your response! The information was useful. |