Distinguishing Plasmids from Chromosomes

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Distinguishing Plasmids from Chromosomes

ganeshS

Hello members

 

I am using Chado for storing Bacterial annotation data.

 

For most organisms, the plasmid and chromosome are separate Genbank records and are loaded as separate unrelated genome features (linked by organism Id).

Is there an easy way to tell which is plasmid and which is chromosome without tampering the genbank/refseq file (the feature cvterms are “region”, which I assume are the defaults, for example can I override the type_id for the top level feature).

 

Has anybody dealt with this scenario ? (Just checking if  there is a best practice for this scenario)

 

Thanks

Ganesh


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Re: Distinguishing Plasmids from Chromosomes

Scott Cain
Hi Ganesh,

I'm guessing you're using the BioPerl tool for converting GenBank records to GFF3?  An unfortunate reality with that converter is that it is less than perfect, and setting the reference sequence to "region" is one example of this.  If you want to continue using it, I would suggest modifying it after it runs to change the feature time to something appropriate (chromosome or plasmid) before loading into Chado.

The other option is to check to see if NCBI has produced GFF3 for your sequences that you can get directly.

Scott



On Fri, Aug 9, 2013 at 10:26 AM, Srinivasamoorthy, Ganesh - INTL <[hidden email]> wrote:

Hello members

 

I am using Chado for storing Bacterial annotation data.

 

For most organisms, the plasmid and chromosome are separate Genbank records and are loaded as separate unrelated genome features (linked by organism Id).

Is there an easy way to tell which is plasmid and which is chromosome without tampering the genbank/refseq file (the feature cvterms are “region”, which I assume are the defaults, for example can I override the type_id for the top level feature).

 

Has anybody dealt with this scenario ? (Just checking if  there is a best practice for this scenario)

 

Thanks

Ganesh


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Ontario Institute for Cancer Research

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Re: Distinguishing Plasmids from Chromosomes

Daniel Quest
When I was at Oak Ridge we annotated hundreds of microbes for the department of energy.  Chances are excellent that your genome is not correctly annotated in the current Genbank file.  I would compare the gene calls to the output from Prodigal (which can generate GFF btw).  And I would strongly encourage you to check out the KBase project.

Chances are that what you are trying to do with Chado overlaps, and this might save you some pain.
Dan

Sent from my iPad

On Aug 9, 2013, at 11:09 AM, Scott Cain <[hidden email]> wrote:

Hi Ganesh,

I'm guessing you're using the BioPerl tool for converting GenBank records to GFF3?  An unfortunate reality with that converter is that it is less than perfect, and setting the reference sequence to "region" is one example of this.  If you want to continue using it, I would suggest modifying it after it runs to change the feature time to something appropriate (chromosome or plasmid) before loading into Chado.

The other option is to check to see if NCBI has produced GFF3 for your sequences that you can get directly.

Scott



On Fri, Aug 9, 2013 at 10:26 AM, Srinivasamoorthy, Ganesh - INTL <[hidden email]> wrote:

Hello members

 

I am using Chado for storing Bacterial annotation data.

 

For most organisms, the plasmid and chromosome are separate Genbank records and are loaded as separate unrelated genome features (linked by organism Id).

Is there an easy way to tell which is plasmid and which is chromosome without tampering the genbank/refseq file (the feature cvterms are “region”, which I assume are the defaults, for example can I override the type_id for the top level feature).

 

Has anybody dealt with this scenario ? (Just checking if  there is a best practice for this scenario)

 

Thanks

Ganesh


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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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