SEA-PHAGES | Phams

Link to this post \| posted 27 Sep, 2017 18:44
cdshaffer	You can't really "merge" the two databases since mysql will just use pham numbers to decide whether to put proteins in the same pham. You want all similar proteins from both phage collections to be put in the same pham when they are similar to each other. The only way to do that is to rerun all the protein comparisons with all the proteins in the database. There is a thread on how to make databases using a web based program called phamDB. See this thread. The program is old enough now that the installation instructions are likely out of date and it will take some tweaking to install but the basic code is still sound. Alternatively, you could use K_phamerate scripts to create your database, you need to check out and use the code at the sea-phages github repository. That repository holds the code currently being used to create the phamerator databases and is being actively maintained by Travis Mavrich. Unfortunately you will have to install and run using command line.

Link to this post | posted 27 Sep, 2017 18:44

You can't really "merge" the two databases since mysql will just use pham numbers to decide whether to put proteins in the same pham. You want all similar proteins from both phage collections to be put in the same pham when they are similar to each other. The only way to do that is to rerun all the protein comparisons with all the proteins in the database.

There is a thread on how to make databases using a web based program called phamDB. See this thread. The program is old enough now that the installation instructions are likely out of date and it will take some tweaking to install but the basic code is still sound.

Alternatively, you could use K_phamerate scripts to create your database, you need to check out and use the code at the sea-phages github repository. That repository holds the code currently being used to create the phamerator databases and is being actively maintained by Travis Mavrich. Unfortunately you will have to install and run using command line.

Link to this post \| posted 27 Sep, 2017 18:49
grosej	appreciate your quick response! Thanks! I have been using phamDB and it is Phabulous. We just have two large databases (50 + phages) that I was hoping to merge.

Link to this post \| posted 27 Sep, 2017 18:49
grosej	appreciate your quick response! Thanks! I have been using phamDB and it is Phabulous. We just have two large databases (50 + phages) that I was hoping to merge.

Link to this post \| posted 29 Sep, 2017 14:16
DanRussell	grosej Hi Dan, I am wondering if there is a way to merge two PhamDB databases, such as by merging the mysql files? thanks! Julianne Grose Hi Juli, I don't know if you can merge two databases easily with PhamDB, but PhamDB definitely makes it easy to add phages that are in the system to other databases in the system without having to re-enter them. You can use the "Add to Database" function. –Dan

Link to this post | posted 29 Sep, 2017 14:16

DanRussell

grosej
Hi Dan,
I am wondering if there is a way to merge two PhamDB databases, such as by merging the mysql files?
thanks!
Julianne Grose

Hi Juli,

I don't know if you can merge two databases easily with PhamDB, but PhamDB definitely makes it easy to add phages that are in the system to other databases in the system without having to re-enter them. You can use the "Add to Database" function.

–Dan

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