SEA-PHAGES | Empty Track

Link to this post \| posted 05 Feb, 2016 15:30
smg366	When we Starterate our Phage, in our report it tell us say Geralt is found in track 153. But then when we go "look" for that track, it does not exist (No colors found, just black lines). Not sure what is going on. If someone wants to try it out, it is for Phage: Geralt_Draft, Gene # 13.

Link to this post \| posted 05 Feb, 2016 18:34
cdshaffer	I will look into this when I can, unfortunately my computer motherboard died last night and I am working from a loaner until it is repaired. Until then my starterator virtual machine is unavailable. It sounds like a couple of other cases I have run with little or no pink. It both of those cases it was not a bug as much as weird corner cases that starterator was not built to handle.

Link to this post \| posted 05 Feb, 2016 21:06
smg366	I hope your computer gets fixed soon! I look forward to hearing you thoughts on our problem. Thank you

Link to this post \| posted 05 Feb, 2016 21:13
smg366	Another problem which may or may not be related. For one of our phages "ShiaLaBeouf" DNA Master says it has 253 genes, but when we run Starterator we get error messages for chunks of genes are missing. My questions is - if Starterator is says it can't find a gene (but it does exist in DNA Master), what does that mean?

Link to this post \| posted 06 Feb, 2016 22:27
cdshaffer	When I look at ShiaLaBeouf in Phamerator I see that it is labeled "ShiaLaBeouf_draft" and that there are 231 genes. The "_draft" means that the phage was run on DNA Master auto-annotation and those auto-annotated genes were incorporated into the database. That database is used by both Starterator and Phamerator so I always look in Phamerator first when debugging starterator. Not sure why your DNA Master has a different number, could be something as simple as the DNA Master total you are looking at includes the tRNA genes (the phamerator database is only counting protein coding genes), or that someone added genes to the DNA Master file. Alternatively, it could be something complicated based on settings or default configuration of your copy of DNA Master compared to the copy that was run to create the auto-annotation that ended up in the database. Another possibility is that there was a glitch that caused an error in the database. Starterator was designed to deal with this situation (i.e. you want to analyze a gene that is not in the phamerator database) by allowing you to enter in coordinates that define a gene (it is the routine listed in the start window as "One unphamerated gene" ). You are supposed to be able to enter the relevant data, phage, phage sequence, gene coordinates and strand and get a result, but I have not had good luck with that routine. It is certainly something that needs work under the hood with the code. Anyway, if you still want to try to track down this discrepancy, then the first step would be to do a careful comparison of the gene list in DNA Master compared to the the Phamerator Database. I extracted the gene list from the phamerator database to help with comparison. You can get the file from this link.

Link to this post | posted 06 Feb, 2016 22:27

cdshaffer

When I look at ShiaLaBeouf in Phamerator I see that it is labeled "ShiaLaBeouf_draft" and that there are 231 genes. The "_draft" means that the phage was run on DNA Master auto-annotation and those auto-annotated genes were incorporated into the database. That database is used by both Starterator and Phamerator so I always look in Phamerator first when debugging starterator.

Not sure why your DNA Master has a different number, could be something as simple as the DNA Master total you are looking at includes the tRNA genes (the phamerator database is only counting protein coding genes), or that someone added genes to the DNA Master file. Alternatively, it could be something complicated based on settings or default configuration of your copy of DNA Master compared to the copy that was run to create the auto-annotation that ended up in the database. Another possibility is that there was a glitch that caused an error in the database.

Starterator was designed to deal with this situation (i.e. you want to analyze a gene that is not in the phamerator database) by allowing you to enter in coordinates that define a gene (it is the routine listed in the start window as "One unphamerated gene" ). You are supposed to be able to enter the relevant data, phage, phage sequence, gene coordinates and strand and get a result, but I have not had good luck with that routine. It is certainly something that needs work under the hood with the code.

Anyway, if you still want to try to track down this discrepancy, then the first step would be to do a careful comparison of the gene list in DNA Master compared to the the Phamerator Database. I extracted the gene list from the phamerator database to help with comparison. You can get the file from this link.

Link to this post \| posted 10 Feb, 2016 06:48
cdshaffer	OK, I ran starterator on Geralt_Draft, Gene # 13. On my version of starterator with my code updatess and with the most recent version of the database it appears to have run OK. Your results may be different than mine with the updated code and a more recent database. Here is the starterator output for Geralt_Draft, Gene # 13. This is an unusual pham in that both geralt 13 and geralt 14 are in the phamily. I suspect that in some phage the two proteins are expressed as a single polypeptide. In this version Geralt 13 is now track 70 and geralt 14 is track 154. There is a minor bug with track numbering in that each page is numbered 1 to 50 so you have to do a little math to find that track 70 should be track 20 on the second page. Track 154 will be the 4th track on the 4th page. This looks to me as a case where the automated analysis does not work well for this very diverse group of proteins so I would just say that Starterator is Not Informative. Although I would say that start 7 @ 8532 is the best supported for geralt 13, and start 61 @ 9035 is the most supported for geralt_14. There are a number of blank tracks after the last track which is track 155, (i.e. the 5th track on page 4) this is a minor bug where empty "tracks" are written to fill the page. Edited 10 Feb, 2016 16:17

Link to this post | posted 10 Feb, 2016 06:48

cdshaffer

OK,
I ran starterator on Geralt_Draft, Gene # 13. On my version of starterator with my code updatess and with the most recent version of the database it appears to have run OK. Your results may be different than mine with the updated code and a more recent database.

Here is the starterator output for Geralt_Draft, Gene # 13.

This is an unusual pham in that both geralt 13 and geralt 14 are in the phamily. I suspect that in some phage the two proteins are expressed as a single polypeptide.

In this version Geralt 13 is now track 70 and geralt 14 is track 154. There is a minor bug with track numbering in that each page is numbered 1 to 50 so you have to do a little math to find that track 70 should be track 20 on the second page. Track 154 will be the 4th track on the 4th page.

This looks to me as a case where the automated analysis does not work well for this very diverse group of proteins so I would just say that Starterator is Not Informative. Although I would say that start 7 @ 8532 is the best supported for geralt 13, and start 61 @ 9035 is the most supported for geralt_14.

There are a number of blank tracks after the last track which is track 155, (i.e. the 5th track on page 4) this is a minor bug where empty "tracks" are written to fill the page.

Edited 10 Feb, 2016 16:17

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