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Recent Activity
All posts created by andrea
| Link to this post | posted 11 Apr, 2022 20:58 | |
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Got it! Thanks so much. It's for GoldenAsh_3. |
Posted in: Starterator → Pham not found in Starterator
| Link to this post | posted 11 Apr, 2022 16:15 | |
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Thanks for letting us know Debbie! We appreciate it. |
Posted in: Starterator → Pham not found in Starterator
| Link to this post | posted 11 Apr, 2022 14:19 | |
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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 |
Posted in: Starterator → Pham not found in Starterator
| Link to this post | posted 05 Apr, 2022 20:01 | |
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Hi Veronique, Thank you very much for your response! The information was useful. |
Posted in: Choosing Start Sites → Cluster G1 Gene Start
| Link to this post | posted 05 Apr, 2022 15:53 | |
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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. |
3.25MbPosted in: Choosing Start Sites → Cluster G1 Gene Start
| Link to this post | posted 18 May, 2021 19:55 | |
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Thank you for your help! |
Posted in: Choosing Start Sites → F1 gene needs help on start site
| Link to this post | posted 07 May, 2021 20:27 | |
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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 | |
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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 | |
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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 | |
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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 |