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Recent Activity
All posts created by debbie
Link to this post | posted 27 Apr, 2018 02:28 | |
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Megan, I agree in your assessment. If I am right in the Golden annotation of the slippery sequence, then Adromedas shows a point mutation obliterating the slippage with a stop codon. While I believe that is where the slippage occurs, it is unclear how that works or what the slippage is. So I am confident calling both genes the TAC genes, but no slippage should be annotated. |
Link to this post | posted 26 Apr, 2018 17:03 | |
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Thanks Welkin! |
Posted in: DNA Master → Saving Blast Results in DNA Master
Link to this post | posted 26 Apr, 2018 12:06 | |
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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. |
Posted in: DNA Master → Saving Blast Results in DNA Master
Link to this post | posted 26 Apr, 2018 11:50 | |
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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. |
Posted in: Web Phamerator → Pham Number Discrepancy
Link to this post | posted 26 Apr, 2018 11:38 | |
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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? |
Posted in: Cluster DE Annotation Tips → Tail assembly chaperones
Link to this post | posted 13 Apr, 2018 14:40 | |
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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). |
Posted in: Gene or not a Gene → Cluster A1 gene question
Link to this post | posted 27 Mar, 2018 01:40 | |
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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. |
Posted in: Cluster DM Annotation Tips → tail assembly chaperone
Link to this post | posted 01 Mar, 2018 17:25 | |
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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! |
Posted in: Cluster AN Annotation Tips → the last gene
Link to this post | posted 20 Feb, 2018 19:32 | |
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Mike, Yes! One of the techs in our lab has tested Soups, KatherineG, and Rosalind on smeg. No evidence of infection was seen. |
Posted in: Host-Range Project → Post Results Here
Link to this post | posted 20 Feb, 2018 12:16 | |
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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. |