SEA-PHAGES | All posts created by adiaz

Link to this post \| posted 10 Apr, 2018 18:08
adiaz	Hi, We just started annotating OneinaGillian (Cluster EG) and I wanted to clarify a couple of things before moving forward. There are some discrepancies on the gene calls made by DNA Master versus those we see in phagesdb (phamerator) and in PECAAN. For example, in phamerator, genes 6 and 8 are listed as being transcribed in the right to left direction while gene 7 is transcribed in the opposite strand from left to right. Based on the Guiding Principles in the lab manual I’m inclined to say that “genes” 6 and 8 are not real since they’re both less than 120 bp long. However, when I look at GeneMark there’s no coding potential on the top three reading frames that would correspond to gene 7. Does this mean that none are actual genes and all three should be deleted or am I missing something? Should we automatically delete anything that’s less than 120 bp even if there’s coding potential but no hits on HHPred and BLAST? On a related note, one of the guiding principles states that each double-stranded segment of DNA is generally part of only one gene. Genes 13 and 14 are on opposite strands and overlap over the entire length of gene 14 (201 base pairs), is this possible? If not, since gene 14 is part of pham 285541 (encodes for a HTH DNA binding protein) while gene 13 is an orphan should we either delete or trim gene 13? It seems like we’re going to run into similar issues in other parts of the genome so I wanted to get your input to insure that we’re on the right track. Thanks for your help, Arturo

Link to this post | posted 10 Apr, 2018 18:08

Hi,

We just started annotating OneinaGillian (Cluster EG) and I wanted to clarify a couple of things before moving forward. There are some discrepancies on the gene calls made by DNA Master versus those we see in phagesdb (phamerator) and in PECAAN.

For example, in phamerator, genes 6 and 8 are listed as being transcribed in the right to left direction while gene 7 is transcribed in the opposite strand from left to right. Based on the Guiding Principles in the lab manual I’m inclined to say that “genes” 6 and 8 are not real since they’re both less than 120 bp long. However, when I look at GeneMark there’s no coding potential on the top three reading frames that would correspond to gene 7. Does this mean that none are actual genes and all three should be deleted or am I missing something? Should we automatically delete anything that’s less than 120 bp even if there’s coding potential but no hits on HHPred and BLAST?

On a related note, one of the guiding principles states that each double-stranded segment of DNA is generally part of only one gene. Genes 13 and 14 are on opposite strands and overlap over the entire length of gene 14 (201 base pairs), is this possible? If not, since gene 14 is part of pham 285541 (encodes for a HTH DNA binding protein) while gene 13 is an orphan should we either delete or trim gene 13?

It seems like we’re going to run into similar issues in other parts of the genome so I wanted to get your input to insure that we’re on the right track.

Thanks for your help,

Arturo

Posted in: Gene or not a Gene → Cluster EG-Annotation guiding principles

Link to this post \| posted 04 Apr, 2018 21:16
adiaz	Hi, As a follow-up question I was wondering what the best way to annotate the first gene of a circularly permuted genome is, in particular with respect to the gap. To be more specific the phage we are currently annotating (KaiHaiDragon) has a 52992 bp long genome but the stop site of the last gene is 52944. Moreover, the start of the first gene is bp 1 meaning that, in theory, if the genome is circularly permuted as announced on PhagesDB there is a 48 bp gap between the last and the first gene. Now, should we treat our genome as circularly permuted or as linear as we annotate it? In other words, for the first gene should we indicate there is a 48 bp gap or no gap at all? Thank you, Arturo

Link to this post | posted 04 Apr, 2018 21:16

adiaz

Hi,

As a follow-up question I was wondering what the best way to annotate the first gene of a circularly permuted genome is, in particular with respect to the gap. To be more specific the phage we are currently annotating (KaiHaiDragon) has a 52992 bp long genome but the stop site of the last gene is 52944. Moreover, the start of the first gene is bp 1 meaning that, in theory, if the genome is circularly permuted as announced on PhagesDB there is a 48 bp gap between the last and the first gene. Now, should we treat our genome as circularly permuted or as linear as we annotate it? In other words, for the first gene should we indicate there is a 48 bp gap or no gap at all?

Thank you,

Arturo

Posted in: Choosing Start Sites → How to choose the start of the first gene for a circularly permuted genome

Recent Activity

All posts created by adiaz