SEA-PHAGES | Analyze our near finished sequence in Phamerator???

Link to this post \| posted 03 Mar, 2016 22:56
GregFrederick@letu.edu	We are almost finished with the annotation of our first two genomes. We have added multiple genes that DNA Master did not call originally. QUESTION: Is there a way to manually input our nearly completed sequence into *Phamerator* to see what how it compares to similar sub-cluster phages? If so, how? If not, this would be a really nice feature to add. (I'm guessing the feature is already available. So please tell me how.) Thanks.

Link to this post | posted 03 Mar, 2016 22:56

We are almost finished with the annotation of our first two genomes. We have added multiple genes that DNA Master did not call originally.

QUESTION: Is there a way to manually input our nearly completed sequence into Phamerator to see what how it compares to similar sub-cluster phages?

If so, how?

If not, this would be a really nice feature to add.

(I'm guessing the feature is already available. So please tell me how.)

Thanks.

Link to this post \| posted 04 Mar, 2016 18:02
cdshaffer	The only graphical way to do this is the recently published PhamDB (see my post in starterator). If you want to go the traditional route, updating the database requires using the python scripts posted by Charles Bowman at his bitbucket repository for k_phamerate. K_phamerate uses a set of programs for database creation that are incompatible with the version of Ubuntu running on the sea-phages virtual machine so you need a different machine to manage databases. I have a virtual machine with all the k-phamerate code installed that I can get to you if you want. This machine is quite a bit larger at almost 12 Gig. So it is not a trivial undertaking. Edited 04 Mar, 2016 18:03

Link to this post | posted 04 Mar, 2016 18:02

cdshaffer

The only graphical way to do this is the recently published PhamDB (see my post in starterator). If you want to go the traditional route, updating the database requires using the python scripts posted by Charles Bowman at his bitbucket repository for k_phamerate. K_phamerate uses a set of programs for database creation that are incompatible with the version of Ubuntu running on the sea-phages virtual machine so you need a different machine to manage databases. I have a virtual machine with all the k-phamerate code installed that I can get to you if you want. This machine is quite a bit larger at almost 12 Gig. So it is not a trivial undertaking.

Edited 04 Mar, 2016 18:03

Link to this post \| posted 07 Mar, 2016 15:25
DanRussell	Hi Greg, If you really want a quick way to check your phages against some others, you could set up a new Phamerator database using the public version of PhamDB we've set up. There's some more info here. I should mention that I would keep all PhamDB databases relatively small for now, fewer than 100 genomes for sure. –Dan Edited 07 Mar, 2016 15:26

Link to this post \| posted 07 Mar, 2016 15:36
GregFrederick@letu.edu	Thanks guys!

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Analyze our near finished sequence in Phamerator???