SEA-PHAGES | 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

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	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

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 16:16
nietof	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 Sorry, here is orpham gene 35 in phamerator. F 59Kb

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

nietof

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

Sorry, here is orpham gene 35 in phamerator.
F

Link to this post \| posted 03 Jun, 2019 18:46
welkin	OK, I completely agree with deleting gene 35 shown in your screenshot from your annotation; I am hoping that Snazzy is the middle genome you are showing here. Could you upload similar pictures of the other site you are concerned about?

Link to this post \| posted 03 Jun, 2019 19:00
nietof	Welkin Here is the other orpham gene 58 in phamerator (gene 57 in DNA Master). This gene 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 it either. It is in the forward strand but all the genes in that region of the genome are on the reverse strand. Fernando 69Kb

Link to this post | posted 03 Jun, 2019 19:00

nietof

Welkin
Here is the other orpham gene 58 in phamerator (gene 57 in DNA Master). This gene 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 it either. It is in the forward strand but all the genes in that region of the genome are on the reverse strand.
Fernando

Link to this post \| posted 05 Jun, 2019 14:31
welkin	yep– absolutely I would delete it. Good instincts! Thanks for asking!

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question on orpham gene on forward strand of Snazzy