SEA-PHAGES | All posts created by nietof

Link to this post \| posted 03 Jun, 2019 16:15
nietof	nietof 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 66Kb

Link to this post | posted 03 Jun, 2019 16:15

nietof
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

Posted in: Gene or not a Gene → question on orpham gene on forward strand of Snazzy

Link to this post \| posted 03 Jun, 2019 16:15
nietof	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 03 Jun, 2019 16:15

nietof

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

Posted in: Gene or not a Gene → question on orpham gene on forward strand of Snazzy

Link to this post \| posted 28 May, 2019 14:47
nietof	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

Posted in: Frameshifts and Introns → Help with frameshift annotation in A1 phage

Link to this post \| posted 24 May, 2019 20:08
nietof	nietof Debbie Jacobs-Sera Fernando, Please send me your DNA Master file and I can show you. If you make sure each region is divisible by 3 it will show you where to cut it. If this is a -1 frameshift (most certainly it is), the last nucleotide of region 1 is the first nucleotide of region 2. Your frame jumping question is not easy to follow when the ribosome is really slipping backwards. debbie Hi Debbie Here is the DNA Master file. Thanks F Debbie I have also attached my rationale for the shift showing the six frame translation and the protein sequences. thanks F 115Kb

Link to this post | posted 24 May, 2019 20:08

nietof

nietof
Debbie Jacobs-Sera
Fernando,
Please send me your DNA Master file and I can show you. If you make sure each region is divisible by 3 it will show you where to cut it. If this is a -1 frameshift (most certainly it is), the last nucleotide of region 1 is the first nucleotide of region 2. Your frame jumping question is not easy to follow when the ribosome is really slipping backwards.
debbie

Hi Debbie
Here is the DNA Master file.
Thanks
F

Debbie
I have also attached my rationale for the shift showing the six frame translation and the protein sequences.
thanks
F

Posted in: Frameshifts and Introns → Help with frameshift annotation in A1 phage

Link to this post \| posted 24 May, 2019 20:07
nietof	Debbie Jacobs-Sera Fernando, Please send me your DNA Master file and I can show you. If you make sure each region is divisible by 3 it will show you where to cut it. If this is a -1 frameshift (most certainly it is), the last nucleotide of region 1 is the first nucleotide of region 2. Your frame jumping question is not easy to follow when the ribosome is really slipping backwards. debbie Hi Debbie Here is the DNA Master file. Thanks F 223Kb

Link to this post | posted 24 May, 2019 20:07

nietof

Debbie Jacobs-Sera
Fernando,
Please send me your DNA Master file and I can show you. If you make sure each region is divisible by 3 it will show you where to cut it. If this is a -1 frameshift (most certainly it is), the last nucleotide of region 1 is the first nucleotide of region 2. Your frame jumping question is not easy to follow when the ribosome is really slipping backwards.
debbie

Hi Debbie
Here is the DNA Master file.
Thanks
F

Posted in: Frameshifts and Introns → Help with frameshift annotation in A1 phage

Link to this post \| posted 24 May, 2019 16:34
nietof	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 24 May, 2019 16:34

nietof

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

Posted in: Frameshifts and Introns → Help with frameshift annotation in A1 phage

Link to this post \| posted 12 Jul, 2018 14:15
nietof	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

Posted in: Host-Range Project → Basic Host Range Project Information

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