Link to this post | posted 26 Apr, 2018 17:03
debbie	Thanks Welkin!

Link to this post | posted 26 Apr, 2018 12:06

debbie

Kayla, Hi. I have fixed the file. I believe the issue involves not providing DNA master enough time to build he database correctly. I used a DNA master utility to repack the file (which has no value until I show you what that means). I couldn't quickly find a protocol to this on the on-line bioinformatics guide. i will get it posted soon. If you are coming to the symposium/faculty meeting, let's chat. 1.39Mb

Link to this post | posted 26 Apr, 2018 11:50
debbie	Andrea, The databases need a moment to talk to one another. Once data is updated in Phamerator, phagesDB will follow. You just caught them in the middle.

Link to this post | posted 26 Apr, 2018 11:38
debbie	Hi. My supporting data is: Sitar_31 has a Pfam hit to TAC (90.6%/40% coverage). It is in the right location for a TAC. The G protein most typically hits homologs (vs T). I could not find the slippery sequence when I checked this genome. Could it be a +1 at position 24240, 24242?

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