SEA-PHAGES | All posts created by cqdiep

Link to this post \| posted 16 Jan, 2019 12:57
cqdiep	Hi Sally, this Mac version of DNA Master doesn't require XQuartz or Wine, right? Thanks.

Posted in: Using WINE to run DNA Master on a Mac → Link to Baylor box

Link to this post \| posted 28 Feb, 2018 17:18
cqdiep	How do we find the following BLAST info for the Notes section? Blast-Start [% coverage] SIF-BLAST [% alignment]

Posted in: DNA Master → BLAST coverage/alignment

Link to this post \| posted 23 Feb, 2018 20:45
cqdiep	Thanks, that makes sense. I also got this response from the Phamerator chat: The draft genomes that are in Phamerator (such as Maroc7_Draft) are directly imported from DNA Master's auto-annotation, which is itself based on Glimmer and GeneMark predictions. The same is true of PECAAN as far as I am aware. So DNA Master, Phamerator, and PECAAN are all showing the output of the same two programs. Why then do the data in Phamerator, DNA Master, and PECAAN not all agree with each other? The Glimmer and GeneMark methods use random subsampling from within a genome to make predictions about where the genes are. Because the random sampling will be different each time the programs are run, the predictions themselves can vary (slightly) each time you run Glimmer or GeneMark. Which output is correct, Phamerator, DNA Master, or PECAAN? While there are clearly issues on the Phamerator map (such as gene 40 that you pointed out), it's likely that all 3 programs are showing annotations that contain mistakes! That's of course why we need to perform manual revisions to the auto-annotation. Hope this helps!

Link to this post | posted 23 Feb, 2018 20:45

cqdiep

Thanks, that makes sense. I also got this response from the Phamerator chat:

The draft genomes that are in Phamerator (such as Maroc7_Draft) are directly imported from DNA Master's auto-annotation, which is itself based on Glimmer and GeneMark predictions. The same is true of PECAAN as far as I am aware. So DNA Master, Phamerator, and PECAAN are all showing the output of the same two programs. Why then do the data in Phamerator, DNA Master, and PECAAN not all agree with each other? The Glimmer and GeneMark methods use random subsampling from within a genome to make predictions about where the genes are. Because the random sampling will be different each time the programs are run, the predictions themselves can vary (slightly) each time you run Glimmer or GeneMark. Which output is correct, Phamerator, DNA Master, or PECAAN? While there are clearly issues on the Phamerator map (such as gene 40 that you pointed out), it's likely that all 3 programs are showing annotations that contain mistakes! That's of course why we need to perform manual revisions to the auto-annotation. Hope this helps!

Posted in: DNA Master → DNA Master vs. Phamerator

Link to this post \| posted 23 Feb, 2018 17:08
cqdiep	I think I found the problem. The map from Phamerator.org has 4 very small extra genes that might be from a mistake. They are inserted into other bigger genes. For example in the attached picture, gene 40 would be a mistake. When I add the sequence into PECAAN, the Phamerator map generated from PECAAN doesn't have those 4 extra genes, which agrees with DNA Master. So should I trust the map from PECAAN and not the one from Phamerator.org? Edited 23 Feb, 2018 17:13 14Kb

Link to this post | posted 23 Feb, 2018 17:08

cqdiep

I think I found the problem. The map from Phamerator.org has 4 very small extra genes that might be from a mistake. They are inserted into other bigger genes. For example in the attached picture, gene 40 would be a mistake.

When I add the sequence into PECAAN, the Phamerator map generated from PECAAN doesn't have those 4 extra genes, which agrees with DNA Master. So should I trust the map from PECAAN and not the one from Phamerator.org?

Edited 23 Feb, 2018 17:13

Posted in: DNA Master → DNA Master vs. Phamerator

Link to this post \| posted 22 Feb, 2018 20:50
cqdiep	We're doing the Maroc7_Draft phage. Phamerator says that there are 95 genes, but autoannotation in DNA Master says there are only 91 genes. How come?

Posted in: DNA Master → DNA Master vs. Phamerator

Link to this post \| posted 23 Jan, 2018 20:55
cqdiep	Got it, thanks. Just wanted to clarify. Welkin Pope Hi Cuong, You will need some way to access Windows for DNA Master. the "SEA Virtual Machine" specifically refers to a frozen Ubuntu image that contains Phamerater and STarteror pre-installed. Best, Welkin

Posted in: DNA Master → Important DNA Master Update

Link to this post \| posted 23 Jan, 2018 20:31
cqdiep	Hi Dan, The recent email from SEA-PHAGES says "INSTALLING THE SEA-PHAGES VIRTUAL MACHINE IS NO LONGER REQUIRED OR RECOMMENDED." But we still need the Virtual Machine to run DNA Master, right? Thanks. Cuong Dan Russell New as of November 15, 2016 Some very important changes have been made to DNA Master to accommodate NCBI's new secure https protocols. Versions of DNA Master from before this date will not be able to connect to NCBI and thus will not be able to auto-annotate genomes or run BLAST. Updating your DNA Master will allow you to be able to use NCBI's new protocols. See this blog post for more information. http://seaphages.org/blog/2016/11/16/dna-master-updated-use-secure-ncbi-connections/ –Dan

Link to this post | posted 23 Jan, 2018 20:31

cqdiep

Hi Dan,

The recent email from SEA-PHAGES says "INSTALLING THE SEA-PHAGES VIRTUAL MACHINE IS NO LONGER REQUIRED OR RECOMMENDED."

But we still need the Virtual Machine to run DNA Master, right? Thanks.

Cuong

Dan Russell
New as of November 15, 2016

Some very important changes have been made to DNA Master to accommodate NCBI's new secure https protocols. Versions of DNA Master from before this date will not be able to connect to NCBI and thus will not be able to auto-annotate genomes or run BLAST.

Updating your DNA Master will allow you to be able to use NCBI's new protocols. See this blog post for more information.

http://seaphages.org/blog/2016/11/16/dna-master-updated-use-secure-ncbi-connections/

–Dan

Posted in: DNA Master → Important DNA Master Update

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