SEA-PHAGES | Cluster G genes spanning the COS site

Link to this post \| posted 11 Feb, 2016 22:53
GregFrederick@letu.edu	In one genome we are seeing overlapping ORFs at the right end of the genome that are curious. See the attached file. DM actually called the long ORF on the reverse ORF and it is in some finished genomes too. But the first called forward ORF in the attached image actually has homologs with known function. The second forward ORF (indicated by the narrow bar) that was not called by DM actually matches with 9 other finished phages on PhagesDB. Question: Is it possible to have a large ORF like this spanning the COS site 'ends'? We BlastP'd it and even though some annotated phages include it, we do not find any putative function. I cannot seem to attach two files here. So I will attach the Genmark coding potential in a second post. Thanks for your thoughts. 23Kb

Link to this post | posted 11 Feb, 2016 22:53

In one genome we are seeing overlapping ORFs at the right end of the genome that are curious. See the attached file.

DM actually called the long ORF on the reverse ORF and it is in some finished genomes too. But the first called forward ORF in the attached image actually has homologs with known function.

The second forward ORF (indicated by the narrow bar) that was not called by DM actually matches with 9 other finished phages on PhagesDB.

Question: Is it possible to have a large ORF like this spanning the COS site 'ends'? We BlastP'd it and even though some annotated phages include it, we do not find any putative function.

I cannot seem to attach two files here. So I will attach the Genmark coding potential in a second post.

Thanks for your thoughts.

Link to this post \| posted 11 Feb, 2016 22:54
GregFrederick@letu.edu	GenMarck smeg Coding Potential for the region. 65Kb

Link to this post \| posted 12 Feb, 2016 15:08
DanRussell	Hi Greg, The coding potential looks sparse on the reverse strand in that region. Quick question: what are the other genomes where that reverse-strand gene is called? Are any (or all) of those still in "_Draft" form? –Dan

Link to this post \| posted 17 Feb, 2016 22:34
GregFrederick@letu.edu	Dan Russell Hi Greg, The coding potential looks sparse on the reverse strand in that region. Quick question: what are the other genomes where that reverse-strand gene is called? Are any (or all) of those still in "_Draft" form? –Dan Dan: I do not have the names in front of me. But when I looked at it with students the other day it appeared that all the hits were in the NCBI Blasts or in 'draft' genomes in the PHAGESBD database. I concluded that those in the NCBI Blast hits were probably "auto-annotated" and deposited without QC (possibly by another group). We determined it was not likely a "real" gene. But it is an incredibly long ORF. So that call was not entirely 'comfortable'.

Link to this post | posted 17 Feb, 2016 22:34

GregFrederick@letu.edu

Dan Russell
Hi Greg,

The coding potential looks sparse on the reverse strand in that region.

Quick question: what are the other genomes where that reverse-strand gene is called? Are any (or all) of those still in "_Draft" form?

–Dan

Dan:

I do not have the names in front of me. But when I looked at it with students the other day it appeared that all the hits were in the NCBI Blasts or in 'draft' genomes in the PHAGESBD database.

I concluded that those in the NCBI Blast hits were probably "auto-annotated" and deposited without QC (possibly by another group). We determined it was not likely a "real" gene. But it is an incredibly long ORF. So that call was not entirely 'comfortable'.

Link to this post \| posted 18 Feb, 2016 16:00
DanRussell	GregFrederick@letu.edu Dan Russell Hi Greg, The coding potential looks sparse on the reverse strand in that region. Quick question: what are the other genomes where that reverse-strand gene is called? Are any (or all) of those still in "_Draft" form? –Dan Dan: I do not have the names in front of me. But when I looked at it with students the other day it appeared that all the hits were in the NCBI Blasts or in 'draft' genomes in the PHAGESBD database. I concluded that those in the NCBI Blast hits were probably "auto-annotated" and deposited without QC (possibly by another group). We determined it was not likely a "real" gene. But it is an incredibly long ORF. So that call was not entirely 'comfortable'. I did end up taking a quick look in Phamerator, and it seemed like the Final genomes all had removed that reverse-strand gene, while the Draft ones still had it. So probably dropping it is the way to go. –Dan

Link to this post | posted 18 Feb, 2016 16:00

DanRussell

GregFrederick@letu.edu
Dan Russell
Hi Greg,

The coding potential looks sparse on the reverse strand in that region.

Quick question: what are the other genomes where that reverse-strand gene is called? Are any (or all) of those still in "_Draft" form?

–Dan

Dan:

I do not have the names in front of me. But when I looked at it with students the other day it appeared that all the hits were in the NCBI Blasts or in 'draft' genomes in the PHAGESBD database.

I concluded that those in the NCBI Blast hits were probably "auto-annotated" and deposited without QC (possibly by another group). We determined it was not likely a "real" gene. But it is an incredibly long ORF. So that call was not entirely 'comfortable'.

I did end up taking a quick look in Phamerator, and it seemed like the Final genomes all had removed that reverse-strand gene, while the Draft ones still had it. So probably dropping it is the way to go.

–Dan

Link to this post \| posted 18 Feb, 2016 17:39
GregFrederick@letu.edu	Dan Russell GregFrederick@letu.edu Dan Russell Hi Greg, The coding potential looks sparse on the reverse strand in that region. Quick question: what are the other genomes where that reverse-strand gene is called? Are any (or all) of those still in "_Draft" form? –Dan Dan: I do not have the names in front of me. But when I looked at it with students the other day it appeared that all the hits were in the NCBI Blasts or in 'draft' genomes in the PHAGESBD database. I concluded that those in the NCBI Blast hits were probably "auto-annotated" and deposited without QC (possibly by another group). We determined it was not likely a "real" gene. But it is an incredibly long ORF. So that call was not entirely 'comfortable'. I did end up taking a quick look in Phamerator, and it seemed like the Final genomes all had removed that reverse-strand gene, while the Draft ones still had it. So probably dropping it is the way to go. –Dan Thanks!

Link to this post | posted 18 Feb, 2016 17:39

GregFrederick@letu.edu

Dan Russell
GregFrederick@letu.edu
Dan Russell
Hi Greg,

The coding potential looks sparse on the reverse strand in that region.

Quick question: what are the other genomes where that reverse-strand gene is called? Are any (or all) of those still in "_Draft" form?

–Dan

Dan:

I do not have the names in front of me. But when I looked at it with students the other day it appeared that all the hits were in the NCBI Blasts or in 'draft' genomes in the PHAGESBD database.

I concluded that those in the NCBI Blast hits were probably "auto-annotated" and deposited without QC (possibly by another group). We determined it was not likely a "real" gene. But it is an incredibly long ORF. So that call was not entirely 'comfortable'.

I did end up taking a quick look in Phamerator, and it seemed like the Final genomes all had removed that reverse-strand gene, while the Draft ones still had it. So probably dropping it is the way to go.

–Dan

Thanks!

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Cluster G genes spanning the COS site