Best way to link short sequences to feature

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Best way to link short sequences to feature

Thomas LETELLIER-2
Hi,

I am working on a GBrowse (v 2.33) and I would like to display short
sequences (between 30 and 50 nucleotides) which are linked to my
features (BAC in my case). I can have one or several sequences per BAC.

I work on a BioDBGFF database schema and I use GFF3 files as input.

My first idea was to put these sequences into the 9 column of the GFF3
and then display them in the "Details report" section. Because of their
length (<50) I think that the display will be clear.


Do you think that there is a best way to handle the display of these
sequences ?

Best regards,

Thomas

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Re: Best way to link short sequences to feature

Scott Cain
Hi Thomas,

I think what you're suggesting is a reasonable approach: the short sequence is just another "attribute" of the feature, so adding it to the ninth column of your GFF is a good idea.

As a side note, I'll mention that since you are using GFF3, you will probably find that you'll get better performance if you use a Bio::DB::SeqFeature::Store database instead of Bio::DB::GFF.

Scott


On Wed, Jun 3, 2015 at 8:22 AM, Thomas LETELLIER <[hidden email]> wrote:
Hi,

I am working on a GBrowse (v 2.33) and I would like to display short
sequences (between 30 and 50 nucleotides) which are linked to my
features (BAC in my case). I can have one or several sequences per BAC.

I work on a BioDBGFF database schema and I use GFF3 files as input.

My first idea was to put these sequences into the 9 column of the GFF3
and then display them in the "Details report" section. Because of their
length (<50) I think that the display will be clear.


Do you think that there is a best way to handle the display of these
sequences ?

Best regards,

Thomas

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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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Re: Best way to link short sequences to feature

Thomas LETELLIER-2
Hi Scott,

thanks a lot, I will try to use Bio::DB::SeqFeature::Store !

Best regards,

Thomas


On 06/03/2015 06:03 PM, Scott Cain wrote:
Hi Thomas,

I think what you're suggesting is a reasonable approach: the short sequence is just another "attribute" of the feature, so adding it to the ninth column of your GFF is a good idea.

As a side note, I'll mention that since you are using GFF3, you will probably find that you'll get better performance if you use a Bio::DB::SeqFeature::Store database instead of Bio::DB::GFF.

Scott


On Wed, Jun 3, 2015 at 8:22 AM, Thomas LETELLIER <[hidden email]> wrote:
Hi,

I am working on a GBrowse (v 2.33) and I would like to display short
sequences (between 30 and 50 nucleotides) which are linked to my
features (BAC in my case). I can have one or several sequences per BAC.

I work on a BioDBGFF database schema and I use GFF3 files as input.

My first idea was to put these sequences into the 9 column of the GFF3
and then display them in the "Details report" section. Because of their
length (<50) I think that the display will be clear.


Do you think that there is a best way to handle the display of these
sequences ?

Best regards,

Thomas

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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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