Link to this post | posted 11 Apr, 2022 20:58
andrea	Got it! Thanks so much. It's for GoldenAsh_3.

Link to this post | posted 11 Apr, 2022 16:15
andrea	Thanks for letting us know Debbie! We appreciate it.

Link to this post | posted 11 Apr, 2022 14:19
andrea	Good morning, We are not able to access Pham 103037 on phagesdb.org or PECAAN. We've been trying since Wednesday, 4/6. Thank you! Andrea

Link to this post | posted 05 Apr, 2022 20:01
andrea	Hi Veronique, Thank you very much for your response! The information was useful.

Link to this post | posted 05 Apr, 2022 15:53

andrea

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 18 May, 2021 19:55
andrea	Thank you for your help!

Link to this post | posted 07 May, 2021 20:27
andrea	Hi Debbie, Thanks for your speedy reply. I was in touch with Kirk to verify our annotation of the Lysin A gene. I made the change in DNA Master to reflect this. Have a great weekend! Andrea

Link to this post | posted 07 May, 2021 14:29

andrea

Hi, We found this in JalFarm20 as well. We tried to change this in PECAAN by deleting the original 2 Lysin A genes (see below) and adding a gene that spanned the entire length of the protein. The pop-up allowed us to enter the proper stop coordinate (28,603) but there was no place to enter the proper start coordinate (26,866), and it did not appear amongst the gene candidates, even when we deleted genes 32, 33, and 34 or just 33+34 first: Gene 32: 26,866-27,360 Forward (Lysin A) Gene 33: 27,847-27,341 Reverse (HNH Endonuclease) Gene 34: 27,884-28,603 Forward (Lysin A) Does anyone know of a way to do this in PECAAN? We were not sure how to use the advanced Join Position for adding a gene, even after reading the PECAAN guide. Or should we delete gene 34 in PECAAN and manually change this in DNA Master? Thank you, Andrea

Link to this post | posted 20 Apr, 2021 16:44
andrea	Thank you, that was very helpful! I just searched on HHpred using took the longer sequence; the extra amino acids did not align to the subject. Andrea

Link to this post | posted 19 Apr, 2021 22:09
andrea	Thanks Debbie! JalFarm20_3 looked very similar to U Pitt's annotation of UncleRicky_3 (e.g. coding potential, length, function) which pointed to retaining the Glimmer and GeneMark call of 797. Hope you're well out there! Andrea