Lee Hughes

GregFrederick@letu.edu
Look at feature 28. In Zaka and CLoudwang3 they apparently called the longest ORF. But based on guiding principles it does not seem "reasonable" because of the entire overlap with feature 27 in those two genomes.

This one is easy to determine in our case because we have a STOP and this is the largest ORF in our case. But it obviously was not in Zaka and Cloudwang3. QUESTION: Do you want us to note those discrepancies so they can be edited? Are previous calls ever corrected/updated based on newer genomic information?

Greg,

I am going to suggest you have a look at the Annotation Guide section 9.4.1 in regard to your question about the feature 27 and 28 overlap you are seeing in Zaka and Cloudwang. This is a special situation.

Lee

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

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

cdshaffer
Many Cluster C phages have a gene that spans the physical end. This gives many computer programs fits, its one of the reasons for Starterator crashing on some phage. Also Phamerator has issues as well (although, thankfully it does not crash) and the whole genome maps created by phamerator often don't include genes of that type.

Glimmer (and maybe GeneMark) will predict genes that span the ends if you tell it that you have a circular genome (DNA Master does do this when it submits the sequence to NCBI for auto-annotation). So it is possible they will show up on your auto-annotation list.

As for finding them, I always have my students check all "largish" regions without genes (say larger than 150 bp) by BLAST. You can have DNA Master locate these "holes" automatically: in DNA Master click the "Validate" button below the feature list, then in the bottom right panel click the "control" tab and then "Locate gray holes" with a size of 150. The resulting list gives the positions and sequences of the "holes" which can then be used to search specifically by BLASTX to the protein database. If students do find hits, I would have them consider the quality of the hit (is it real or spurious) and examine the region carefully for a missing gene (evidence would include coding potential and the presence of an ORF that does not have too much overlap with other genes).

Welkin Pope
Can you give me some scenarios that might lead one to select the "longest 'unreasonable' ORF" or a "shorter-than-longest reasonable ORF"?

Sure. when the comparative genomics, like through STarterator or BLAST, shows that the start that gives you the longest ORF in your phage gene in your genome isn't present in closely related genes, and one that gives you a shorter gene product is. Solid comparative data trumps everything.

cdshaffer
Not a problem really, takes about 3 minutes to start things rolling and then everything runs in the background. Then takes another 3 or 4 minutes to post to box and copy the shared link.

Gideon did run just fine so it is likely a known bug.