SEA-PHAGES | DNA MASTER vs PhageDB: Gene Coordinates

Link to this post \| posted 22 Aug, 2020 17:29
Juan.MartinezV	Hello, Some of my new classmates and I are annotating a phage from last semester (to practice). After running the auto annotation we have 93 genes on DNA MASTER and according to PhagesDB there are 89, the coordinates from these genes are different on both sites. One of the "quality" steps to have in mind when we are about to finish the annotation is "to have" the same number of genes on DNA MASTER and PhageDB, so my questions are: 1) Is PhageDB the ultimate reference to know how many genes there has to be in a genome? 2) Do the coordinates have to be the same on DNA MASTER and PhagesDB? Thanks! JM Edited 22 Aug, 2020 17:30

Link to this post | posted 22 Aug, 2020 17:29

Hello,

Some of my new classmates and I are annotating a phage from last semester (to practice). After running the auto annotation we have 93 genes on DNA MASTER and according to PhagesDB there are 89, the coordinates from these genes are different on both sites. One of the "quality" steps to have in mind when we are about to finish the annotation is "to have" the same number of genes on DNA MASTER and PhageDB, so my questions are:

1) Is PhageDB the ultimate reference to know how many genes there has to be in a genome?
2) Do the coordinates have to be the same on DNA MASTER and PhagesDB?

Thanks!

Edited 22 Aug, 2020 17:30

Link to this post \| posted 23 Aug, 2020 02:45
debbie	Juan, Great questions. There are a number of explanations for this. In order to best answer this, I need to know a couple of things. What school are you asking from? What phage are you talking about? Have you read the Bioinformatics Guide about auto-annotation? debbie

Link to this post \| posted 23 Aug, 2020 02:54
Juan.MartinezV	Hello Debbie We are from Mexico (Universidad Autonoma de Nuevo Leon) and we are talking about Puknovik (https://phagesdb.org/phages/Pukovnik/). I read the Bioinformatics Guide and says a lot about delete or add genes depending on the information from the other tools. For what I remember, the phagesdb was the references but I wanted to be sure about this. If there is some article that I should follow on the guide, I'll be more than happy to check it! Thanks JM

Link to this post | posted 23 Aug, 2020 02:54

Juan.MartinezV

Hello Debbie

We are from Mexico (Universidad Autonoma de Nuevo Leon) and we are talking about Puknovik (https://phagesdb.org/phages/Pukovnik/). I read the Bioinformatics Guide and says a lot about delete or add genes depending on the information from the other tools. For what I remember, the phagesdb was the references but I wanted to be sure about this. If there is some article that I should follow on the guide, I'll be more than happy to check it!

Thanks

Link to this post \| posted 23 Aug, 2020 03:17
debbie	Juan, Mycobacterium phage Pukovnik was found in 2005 and is in GenBank and part of numerous publications, including this one. https://pubmed.ncbi.nlm.nih.gov/24112940/ It is no longer in its draft form but has been hand curated and modified. In addition, there is experimental data to support some of the gene calls. Because Pukovnik is in GenBank, PhagesDB genes reflect that record. A DNA Master auto-annotation represents the Draft version of a file that is then curated by annotators like you. PhagesDB will report the data that that should be most complete, so if it is in GenBank. However, if it is a new genome, phageDB will post the draft information. In addition, if the data is in draft form, Phages DB (and Phamerator) may not match your DNA Master auto-annotation because of the way that the data is generated. Edited 24 Aug, 2020 16:05

Link to this post | posted 23 Aug, 2020 03:17

debbie

Juan,
Mycobacterium phage Pukovnik was found in 2005 and is in GenBank and part of numerous publications, including this one. https://pubmed.ncbi.nlm.nih.gov/24112940/
It is no longer in its draft form but has been hand curated and modified. In addition, there is experimental data to support some of the gene calls.
Because Pukovnik is in GenBank, PhagesDB genes reflect that record. A DNA Master auto-annotation represents the Draft version of a file that is then curated by annotators like you.

PhagesDB will report the data that that should be most complete, so if it is in GenBank. However, if it is a new genome, phageDB will post the draft information. In addition, if the data is in draft form, Phages DB (and Phamerator) may not match your DNA Master auto-annotation because of the way that the data is generated.

Edited 24 Aug, 2020 16:05

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DNA MASTER vs PhageDB: Gene Coordinates