Link to this post | posted 13 Apr, 2018 14:40
debbie	I think that this is a gene and the coding potential says to use the longest start. I did not find Starterator helpful. Blast at PhagesDB and NCBI along with HHpred results did not show any functions. CLUSTALW does show the 'insert' you mention, but i don't believe there is anything to say about it at this point (not knowing function or relevance).

Link to this post | posted 27 Mar, 2018 01:40
debbie	I think that at this time, we can only call the G of the G/T frameshift because, there is no start codon in the frame of the T gene nor can I find a slippery sequence as per published literature. So for now, I recommend that we only call the G gene as a tail assembly chaperone if you have supporting evidence. Continue to look for a slippery sequence. Edited 27 Mar, 2018 01:42 35Kb

Link to this post | posted 01 Mar, 2018 17:25
debbie	The last gene in these genomes is an HNH endonuclease. The auto-annotated gene in that space is not it and it is usually on the opposite strand!

Link to this post | posted 20 Feb, 2018 19:32
debbie	Mike, Yes! One of the techs in our lab has tested Soups, KatherineG, and Rosalind on smeg. No evidence of infection was seen.

Link to this post | posted 20 Feb, 2018 12:16
debbie	Evan, I think these are the tail assembly chaperone genes, but I could not locate the slippery sequence. If you have a suggestion, let me know.

Link to this post | posted 20 Jan, 2018 19:43

debbie

Hi to all who have a Microbacterium phage! It is an exciting time in Actinobacteriophage discovery! We have learned that using comparative genomics to understand the genome content of each phage is profitable. It is great to compare your genome annotation(s) to genomes that have been previously called and QC'd. If you find that you are annotating a genome that has no final genome annotations with which to compare, do not go it alone! I have two considerations for you to follow: 1. You have much comparative data if there are draft genomes in the database. Do not ignore them. You will want to compare the genes and their starts using Phamerator, Starterator and other alignment tools. Do not ignore them simply because they are drafts. (Your evaluation will be different from a comparison to a final annotation, but the draft comparative data will inform your decision-making. In fact, Starterator will become your best friend! 2. Begin conversations with the owners of those drafts on the Forums to collaboratively work out the best annotations. Happy Annotating! Edited 22 Jan, 2018 18:35

Link to this post | posted 19 Dec, 2017 21:40
debbie	Mike, Do you plan to phagehunt and to use the 30 phages (and whatever else you may have) with a new host? Do you know which host you would like to use?

Link to this post | posted 17 Oct, 2017 20:22
debbie	Tom, Hi. Not sure if I can help, but let's see. What build of DNA Master are you running? It should be Build 2529. What fasta file are you using? If it will help, you can call me. debbie

Link to this post | posted 10 Oct, 2017 14:08
debbie	I asked the folks who are running the auto-annotations to check their settings. They have confirmed that they are using the same settings/versions. It is my understanding that Glimmer and GeneMark use a random 'sample' of the genome and to the best of my knowledge that explains the discrepancies. That explains why hand curation and the work we do with these genomes is so necessary.

Link to this post | posted 11 Sep, 2017 19:31

debbie

Recently, it was brought to my attention that the Wintermute lysate is contaminated. Upon investigation, it has been determined that Wintermute IS contaminated with Fionbharth. My apologies. Teachable moment: Whenever you receive a lysate, please always do the following: 1. Freeze the lysate for long term use. 2. Make a high titer lysate for your own use. Use preferred microbiology practice and make your phage lysate from a single plaque. PCR verify that plaque and your lysate. 3. Freeze aliquots of your high titer lysate for future use. debbie Edited 11 Sep, 2017 19:32