Link to this post | posted 08 Apr, 2021 14:42

smg366

Within the A4 phages, is it possible for the tail assembly chaperone gene not to have a frameshift and exist as two different genes, which is the way the genes have been annotated in LeoAvram and NorthStar. I am working on annotating phage LochMonster which is similar to these phages, but as all the other A4 have a frameshift, it seems wrong not to call a frameshift. I have compared the proteins and DNA and can't find a frameshift mutation. I wanted to double check before making the call that there is no frameshift. Thanks, Susan

Link to this post | posted 08 Apr, 2021 14:42

smg366

Within the A4 phages, is it possible for the tail assembly chaperone gene not to have a frameshift and exist as two different genes, which is the way the genes have been annotated in LeoAvram and NorthStar. I am working on annotating phage LochMonster which is similar to these phages, but as all the other A4 have a frameshift, it seems wrong not to call a frameshift. I have compared the proteins and DNA and can't find a frameshift mutation. I wanted to double check before making the call that there is no frameshift. Thanks, Susan

Link to this post | posted 11 Mar, 2020 20:13

smg366

Drexel University is on the quarter system. Our 10 week Spring term starts in 3 weeks time and we usually have the students work on independent wet lab projects. I have been asked to plan a 10 week online course, for our 90 SEA-PHAGE students (as a contingency plan). They have already annotated 8 genomes and written up draft Microbiology Resource Announcement articles describing their phages. Does anyone have any ideas for phage related online materials or assignments, which can build upon the annotations or their knowledge from isolating phages? Any ideas would be much appreciate. Susan Gurney

Link to this post | posted 04 Mar, 2020 18:22
smg366	Thank you Debbie, I didn't have the genetic code selected. Sorry to trouble you. Susan

Link to this post | posted 04 Mar, 2020 17:10

smg366

I am an expedited submitter, and have been doing the validation process for a number of phages without any errors appearing. I have just tired to validate phage BeautPeep30, and I have a lot of errors. But I can't see any issues on the DNA Master final file. Errors: ERROR: valid [SEQ_FEAT.StartCodon] Illegal start codon used. Wrong genetic code [1] or protein should be partial FEATURE: CDS: hypothetical protein [lcl|BeautPeep30:c40034-39648] [lcl|BeautPeep30: raw, dna len= 41809] -> [lcl|BeautPeep30_60] ERROR: valid [SEQ_FEAT.StartCodon] Illegal start codon used. Wrong genetic code [1] or protein should be partial FEATURE: CDS: hypothetical protein [lcl|BeautPeep30:c40390-40031] [lcl|BeautPeep30: raw, dna len= 41809] -> [lcl|BeautPeep30_61] ERROR: valid [SEQ_INST.BadProteinStart] gap symbol at start of protein sequence (2 - terminase) BIOSEQ: lcl|BeautPeep30_2: raw, aa len= 466 ERROR: valid [SEQ_INST.BadProteinStart] gap symbol at start of protein sequence (7 - hypothetical protein) BIOSEQ: lcl|BeautPeep30_7: raw, aa len= 82 Can anyone see what I did incorrectly? I have attached the final DNA Master file. Many thanks, Susan 28Kb

Link to this post | posted 14 Dec, 2019 02:20

smg366

I am using DNA Master Version 5.23.2 from 11 Dec 2017. For the past few weeks, when a run the auto-annotation I get a blank features table. Today I decided to export the information from PECAAN to populate the table. This worked, but when I close the file and try to reopen it I get a "range check error". I have tried on multiple computers, but can't get the auto-annotation to work. When I try to run the update, that also doesn't work. The update runs, but there is no window saying I should close DNA Master. When I eventually try to close it, it has not updated. Any help would be much appreciated. Thanks, Susan

Link to this post | posted 25 Feb, 2019 23:27
smg366	Thank you, I will make sure they are included in our phages. Susan

Link to this post | posted 25 Feb, 2019 03:35

smg366

We are annotating some EA1 phages (host was Microbacterium foliorum). In phage PrincePhergus both Aragorn and tRNAscan predict 1 tRNA. We want to call this tRNA, but when I compare it to phages Golden and Koji on PECAAN, they both show 1 tRNA predicted by both Aragorn and tRNAscan, but they don't call it in their final annotation. My impression was that we call any tRNA gene which was identified by Aragorn. Is there some reason that it was not called in these other phages? Thanks, Susan

Link to this post | posted 14 May, 2018 18:01

smg366

I am using the new export function on PECAAN and I have just noticed that the tRNA notes section and the Conserved Domain Database information is not being converted into my notes section within DNA Master. How can I get this information across? Also, for the CDD information, in the new notes template there doesn't seem to be anywhere to include CDD results. Do we no longer need to report these? If we do report them, how/where should we do it? Thanks, Susan

Link to this post | posted 27 Apr, 2018 16:35

smg366

I confused about the functional assignment for gp8 and gp9 in the B1 cluster. My phage genome is identical to phages JacAttac and Newman at this region of the genome. But different phages have assigned different functions to the same genes. In phage Newman gp8 has been assigned the function Portal protein, however in phage JacAttac gene 8 has NKF, and in Newman gp9 has been assigned Portal protein (similar to phages Chah, Badfish and many other B1 cluters). For my phage (Vaticameos) the Portal function for gp8 is supported by PhagedDB BLAST, HHPRED, but NCBIBLAST and Phamerator say NKF. For gp9 in Vaticameos, PhagesDB BLAST says Capsid Morphogenesis Protein, where as NCBIBLAST and Phamerator say Portal protein. In terms of analyzing the evidence, how should I prioritize the functional results for gp8 and gp9?