Gbrowse Search Options & Display Chromosome specific features

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Gbrowse Search Options & Display Chromosome specific features

sjyap
Hi All,

  I am using gbrowse 2.x. I have a few question on the search and display functionality of gbrwose:

1.  Can I search specifically to what data type or source in the database? I am using Chado schema.
2.  Can search genes specifically to a particular chromosome? Or can I just display all the features found in a particular chromosome/scaffold in the return search interface where we can see the "Name, Type, Description, Position and Match Score" page?

 Thanks in advanced for all your input.

Thanks and regards,
Soon Joo



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Re: Gbrowse Search Options & Display Chromosome specific features

Scott Cain
Hi Soon Joo,

I'll put answers inline below.

Scott


On Sun, Dec 18, 2011 at 11:22 PM, Soon Joo Yap
<[hidden email]> wrote:
> Hi All,
>
>   I am using gbrowse 2.x. I have a few question on the search and
> display functionality of gbrwose:
>
> 1.  Can I search specifically to what data type or source in the database? I
> am using Chado schema.

You can specify feature type in the search by putting it before a
colon with your search term.  For example, these work for me:

  gene:YCR02*
  gene:YAL031C

I don't think you can add source in the search box.

> 2.  Can search genes specifically to a particular chromosome? Or can I just
> display all the features found in a particular chromosome/scaffold in the
> return search interface where we can see the "Name, Type, Description,
> Position and Match Score" page?

The simple search box does not allow for this either, however it is
possible to write plugins for GBrowse that filters features, and it
might be possible to write a more advance search tool that makes use
of a filter plugin (but obviously I've never tried).

>
>  Thanks in advanced for all your input.
>
> Thanks and regards,
> Soon Joo
>
>
>
> ------------------------------------------------------------------------------
> Learn Windows Azure Live!  Tuesday, Dec 13, 2011
> Microsoft is holding a special Learn Windows Azure training event for
> developers. It will provide a great way to learn Windows Azure and what it
> provides. You can attend the event by watching it streamed LIVE online.
> Learn more at http://p.sf.net/sfu/ms-windowsazure
> _______________________________________________
> Gmod-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>



--
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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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developers. It will provide a great way to learn Windows Azure and what it
provides. You can attend the event by watching it streamed LIVE online.  
Learn more at http://p.sf.net/sfu/ms-windowsazure
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