Link to this post | posted 09 Apr, 2018 16:08

kaylafast

We are working on the frameshift in the C1 phage Cane17 (gp123 and gp124). The DNA Master file is attached. We've used C1 phages Phox and ZygoTaiga as a reference. I have narrowed down the frameshift to occur somewhere between 72802-72805 in Cane17 where the shift is in one of the As in a sequence of 4 As. Phox and ZygoTaiga do not agree on which A is the correct one to be counted twice. I think that choosing any of the 4 As gives the same result. Is there a way to be more certain which A is the correct frameshift site? Also, in DNA Master I get the error "72290 - 72817 and share a 5' (upstream) coordinate". That error makes sense after adding the frameshift, and I've read forum posts from others getting the same error. Is there a way to get rid of this error? 1.16Mb

Link to this post | posted 23 Mar, 2018 20:12

kaylafast

I've read the previous responses in this post, but still feel conflicted about the correct formatting for the complete notes and minimalistic files. I've been following the instructions in the online SEA-PHAGES Bioinformatics Guide under the tab "Documenting Your Annotation" and the cover sheet requirements. For the Complete Notes File: Attached is a screenshot of what my files looks like now. I have copied official functions to the function field because of the following line in the online guide, 'All functions are from the official SEA-PHAGES list and are written in the “Function field”. Functions do not have a hard return after them.' Is the "Function Field" the field/box in DNA Master or the "F" slot in the notes? For the Minimal File: Here I followed the instructions in the online guide section called "Final .dnam5 file: Minimal version". Following these steps filled the product field and leaves the function field and notes empty. I'd appreciate help pointing out if there is anything that I should change. 513Kb

Link to this post | posted 21 Mar, 2018 16:22
kaylafast	Thanks!

Link to this post | posted 21 Mar, 2018 15:46
kaylafast	Is there any update on what the most appropriate function call for Pham 5142 is (something along the lines of phospholipase A2 domain protein, PLA2)? My B1 phage (Kwksand96 gp74) shows HHPred results very similar to Kristen's with no phospholipase hits, but many in phagesDB and NCBI Blast. I don't see a close function match in the official function list.

Link to this post | posted 13 Mar, 2018 18:02

kaylafast

We are working on the function assignment for a gene in a C1 phage (Cane17 48994-49932). I see two functions with some support, but neither has an exact match in the official list. Any suggestions on which function to choose? endonuclease: HHPred matches a few endonucleases(Holliday junction resolvases)with >98% probability, 29-30 % alignment, examples: d1m0da_ and 1M0D_D. Holliday junction resolvase is an approved function. PhagesDB blast shows 1 hit with 1:1, 96% alignment, e=0.0 and four with much worse matches. zinc-finger DNA binding domain: PhagesDB blast shows 2 hits with 1:1, 96 %alignment, and e=0.0; six with 1:12-129:44, 54-95% alignment, and e= e-101-0.0. Edited 13 Mar, 2018 18:03

Link to this post | posted 31 May, 2017 15:54
kaylafast	Debbie Jacobs-Sera Kayla, Great! Have you tried to phage hunt on your strain? debbie No, we haven't done that.

Link to this post | posted 31 May, 2017 15:16

kaylafast

Hi Debbie, I did repeat Che9c, Island3, Rey, Nanosmite, and Peaches with similar results. The only details I have about this Mycobacterium smegmatis strain are the NRRL accession number (B-2401, VAS accession number (477), and author citation-(Trevisan 1889) Lehmann and Neumann 1899. I haven't had any luck finding anything else about that strain. I will see about redoing Tweety and Jeon on a full plate. Thanks, Kayla

Link to this post | posted 30 May, 2017 16:01
kaylafast	Attached are the Host Range results from the University of West Alabama for M. smegmatis B-24018. The summary results have been added to the Summary Goggle Spreadsheet. Edited 30 May, 2017 16:02 1.35Mb 1.51Mb

Link to this post | posted 13 Mar, 2017 15:46
kaylafast	Thanks Debbie!

Link to this post | posted 13 Mar, 2017 14:09
kaylafast	What size plate is typically used for the host range project? We are having difficulty fitting all 8 dilutions plus a negative control in a row onto a 100mm X 15mm plate. Wondered if other people were just using bigger plates.