CTG Not Valid Start Codon

[PhageGuy]

Hi all,

In my database some of the genomes use CTG as their start codon. This appears to not be a valid start codon in PhamDB. Is there any way I can edit the parameters of acceptable start codons to include CTG so I can add these phages to the database?

Thanks!

[jglamine]

Hi, thanks for reporting this issue.

I'm not actively developing PhamDB at this point, but if you want to submit a pull request I'd be happy to merge it.

The relevant line of code to change would be here:

https://github.com/jglamine/phamdb/blob/master/pham/genbank.py#L531

I'm not sure what the implications are in terms of adding that as a default start codon - would this cause problems for people who don't want CTG as a start codon?

Another work around would be to not use CTG as your start codon, but I'm aware that this isn't really helpful advice.

[PhageGuy]

Thanks for the response!

If I were to change the code would the change be implemented immediately, or would I have to redownload docker or something along those lines? Also, I believe that any organism that doesn't aim to have CTG as a start simply wouldn't. Start codons are highly conserved so I couldn't see a situation where someone who doesn't already want to use CTG would have an organism who's start is CTG and then gets through the filter via this change.

Thanks again

[jglamine]

You could make the change on your own computer and then publish your own docker image. If I merged the change I could publish the docker image. I'm fine with adding CTG as a start codon, worst case scenario some people accidentally have it as a start codon and don't notice.

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On Oct 18, 2017 10:03 AM, "PhageGuy" ***@***.***> wrote: Thanks for the response! If I were to change the code would the change be implemented immediately, or would I have to redownload docker or something along those lines? Also, I believe that any organism that doesn't aim to have CTG as a start simply wouldn't. Start codons are highly conserved so I couldn't see a situation where someone who doesn't already want to use CTG would have an organism who's start is CTG and then gets through the filter via this change. Thanks again — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#8 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AA0sE-5v9QrQ3OczWrNNNWucpPew_UAdks5sthNJgaJpZM4P9BQX> .

[PhageGuy]

Ok great!

So being I am a biologist rather than a computer scientist what if anything would I need to do for you so that the code can be changed to allow CTG as a valid start?

Thanks again for your help!

[jglamine]

Sorry for the late reply! Unfortunately I don't have a lot of free time to help walk you through the steps.

If there's someone in your organization who is familiar with computer science or software development, you might want to ask them for help. They'll need to know about git and Github at a minimum, and knowledge of Python and Docker would also be useful.

[PhageGuy]

Hi jglamine,

Just bumping on the issue thread as well that I made the merge request so that the docker image can be published with CTG.

Thanks!

[jglamine]

Ok, I'll take a look this weekend.

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On Wed, Nov 8, 2017 at 10:59 AM, PhageGuy ***@***.***> wrote: Hi jglamine, Just bumping on the issue thread as well that I made the merge request so that the docker image can be published with CTG. Thanks! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#8 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AA0sE9jzWOv9aAqhuUQbwKKFA8DQpHZjks5s0d30gaJpZM4P9BQX> .

[PhageGuy]

Thanks so much! Bobby Weisensee Gettysburg College 18' Merck & Co. Medical Oncology Intern Kustos, Theta Chapter, Sigma Chi

________________________________ From: James Lamine <notifications@github.com> Sent: Wednesday, November 8, 2017 8:09:20 PM To: jglamine/phamdb Cc: Robert A. Weisensee; Author Subject: Re: [jglamine/phamdb] CTG Not Valid Start Codon (#8) Ok, I'll take a look this weekend.

On Wed, Nov 8, 2017 at 10:59 AM, PhageGuy ***@***.***> wrote: Hi jglamine, Just bumping on the issue thread as well that I made the merge request so that the docker image can be published with CTG. Thanks! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#8 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AA0sE9jzWOv9aAqhuUQbwKKFA8DQpHZjks5s0d30gaJpZM4P9BQX> .

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#8 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AfXSujLpEB3ZJYvP4NXpM6GW1KIhKiskks5s0lDAgaJpZM4P9BQX>.

[PhageGuy]

Good evening, just bumping for the merge request with CTG to complete our database

Thanks!

[jglamine]

I've merged you change, but I'm running into a bunch of errors trying to publish a new image - it's been two years, so some stuff which used to work doesn't anymore. I'd love to help, but I don't really have the time or energy to work through these issues.

My advice is to find a workaround, perhaps by editing your genbank files or using legacy phamerator without phamdb.