Link to this post | posted 02 Jun, 2025 17:26
byrumc@cofc.edu	Thanks so much for your help with this, Chris! I'll contact Dan.

Link to this post | posted 01 Jun, 2025 05:44
byrumc@cofc.edu	I'm trying to revise an annotation paper and the reviewer asked whether the genome is rotated (under the topic "genome assembly." Could someone clarify what they're asking?

Link to this post | posted 01 Jun, 2025 05:44
byrumc@cofc.edu	I'm trying to revise an annotation paper and the reviewer asked whether the genome is rotated (under the topic "genome assembly." Could someone clarify what they're asking?

Link to this post | posted 01 Jun, 2025 05:44
byrumc@cofc.edu	I'm trying to revise an annotation paper and the reviewer asked whether the genome is rotated (under the topic "genome assembly." Could someone clarify what they're asking?

Link to this post | posted 28 May, 2025 18:09
byrumc@cofc.edu	Hi Debbie, Thanks for mentioning this. I checked the Genbank files for Hashim76 (both the nucleotide file and the SRA file), but they just say unclassified bacterial virus. Since it is a tailed virus, I'm assuming it would be safe to say it is a member of the class Caudoviricetes and, as the second reviewer suggested, I could say it has siphovirus morphology.

Link to this post | posted 27 May, 2025 20:22
byrumc@cofc.edu	Virus family classification based on ICTV standards was also requested on my recent submission to Microbiology Resource Announcements. Thanks for the tips.

Link to this post | posted 19 Dec, 2024 22:47

byrumc@cofc.edu

In some of the L3 phages the chaperone protein frameshift is annotated as a +1 frameshift and in others it is annotated as a -2 frameshift. When annotated as a -2 frameshift, the sequence is HFFFGSK. When annotated as a +1 frameshift the sequence is HFFGSK. Both seem equally feasible. Is there any mass spec evidence that one is more likely than the other? The slippery sequence is TTTTTTC…but it involves a shift from the 2nd reading frame to the 1st instead of a shift from the 2nd reading frame to the 3rd.

Link to this post | posted 12 Aug, 2021 20:05
byrumc@cofc.edu	Thanks, Dan! That helps! Christine

Link to this post | posted 12 Aug, 2021 20:05
byrumc@cofc.edu	Thanks, Dan! That helps! Christine

Link to this post | posted 12 Aug, 2021 19:11
byrumc@cofc.edu	Quick question…During assembly of the genomes, is there a program used to trim the reads or is there no need to trim the 150-bp single end reads before looking at them in Newbler? Thanks! Christine