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Recent Activity
JustinA posted in Plaques appear on spot test, don't appear in titer
Viknesh Sivanathan posted in Plaques appear on spot test, don't appear in titer
JustinA posted in Plaques appear on spot test, don't appear in titer
Viknesh Sivanathan posted in Plaques appear on spot test, don't appear in titer
RyanWheeler posted in Plaques appear on spot test, don't appear in titer
All posts created by nietof
Link to this post | posted 03 Jun, 2019 16:15 | |
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nietof |
Link to this post | posted 03 Jun, 2019 16:15 | |
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Hi Snazzy Gene 58 in phamerator is called as a forward gene overlapping with gene 57 a reverse gnee in a section of the genome where all the genes are coded on the reverse strand. Glimmer calls it in DNA Master but as gene 57 (difference in gene numbers between phagesDB/phamerator and DNA master is due to another questionable orpham gene 35 called only in PhagesDB/phamerator, but not called by Glimmer in DNA Master and with very poor CP in GeneMarkS). Gene 57 is called by Glimmer not by GeneMark but with strong CP in GeneMarkS. There is no functional assignment in BlastP and poor hits in HHPred, smallest E value is 31. We are inclined not to call either one of these orpham genes. Fernando |
Link to this post | posted 28 May, 2019 14:47 | |
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Debbie Somehow I had a misconception that a shift between 1 and 3 frames required a two base shift either back or forth(-2 or +2). It took me looking at the closely related genomes to realize that I was wrong. So I think I just needed confirmation on this one. Thank you. F |
Link to this post | posted 24 May, 2019 20:08 | |
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nietofDebbie Jacobs-Sera Debbie I have also attached my rationale for the shift showing the six frame translation and the protein sequences. thanks F |
Link to this post | posted 24 May, 2019 20:07 | |
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Debbie Jacobs-Sera Hi Debbie Here is the DNA Master file. Thanks F |
Link to this post | posted 24 May, 2019 16:34 | |
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Hi We are working on Snazzy. The tail assembly chaperones are genes 20 and 21 both on the forward strand but gene 20 ORF is in the 1 and 21 in the 3 frame. We located a GGGGGAA slippery sequence at 15336 in 20. We thought the ribosome would read the GGG at position 15337-15339 in frame 1 for a G and then slip back and read again GGA in frame 3 for another G. It yields 266 residues. When I blastp the product after the frameshift it aligns 100%, 100% coverage and 99.6% identity(residue 69 is different) to Violet tail assembly chaperone protein with no gaps. The sequence in the region where the shift happens aligns perfectly with that of Violet. Am I looking at this right? Is it a -1 frameshift but the ribosome jumps from frame 1 to 3. Thank you Fernando |
Link to this post | posted 12 Jul, 2018 14:15 | |
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Hi folks I am working with a group of energetic highschoolers from LI, NY. They are interested in testing host range for their phage isolates using smeg. How broad is the range of bacterial hosts they can test? Should they stick to closely related bacteria? Thank you Fernando |