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question on orpham gene on forward strand of Snazzy

| 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
| 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 03 Jun, 2019 16:16
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
| posted 03 Jun, 2019 18:46
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?
| posted 03 Jun, 2019 19:00
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
| posted 05 Jun, 2019 14:31
yep– absolutely I would delete it. Good instincts!

Thanks for asking!
 
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