[Gmod-help] Re: [Gmod-gbrowse] Question about Linking and how "gbrowse_details" works

[Fariba M]

Hi,
Thanks for your answers.But in fact, for the gbrowse details page, I would like to have:
1.  the spliced coding sequence (i.e. the CDS).  For example, for g2928, each of the exons appears as a pink box.  We would like to join (splice) the text from the pink boxes, end to end, removing the non-pink (intron) sequence in between each exon and print out a string on the report called the CDS. 2. the translation of the CDS from RNA into protein (single-letter amino acid code). 
I don't know how GBrowse should be configured to do these. I would be so grateful if you can help me.
Thanks,Fariba 


--- On Wed, 8/25/10, Scott Cain <scott at scottcain.net> wrote:

From: Scott Cain <scott at scottcain.net>
Subject: Re: [Gmod-gbrowse] Question about Linking and how "gbrowse_details" works
To: "Dave Clements, GMOD Help Desk" <help at gmod.org>
Cc: "Fariba M" <fariba_mahdavifard at yahoo.com>, gmod-gbrowse at lists.sourceforge.net
Date: Wednesday, August 25, 2010, 7:00 PM

Hi Fariba,

I suspect you are referring to the extracted sequence for the feature that appears at the bottom of the gbrowse_details page.  The script is just using the reference sequence in the database and the start and stop data for the feature (and child features if present) and extracting the sequence from the database (via bioperl).  I agree with Dave that you should look into using the config file to modify how the details page looks before hacking away at the script (though the details page script isn't terribly complicated).


Scott


On Tue, Aug 24, 2010 at 7:25 PM, Dave Clements, GMOD Help Desk <help at gmod.org> wrote:

Hi Fariba,
You can control some things on the gbrowse_details page using the methods listed at:
http://gmod.org/wiki/GBrowse_Configuration_HOWTO#Controlling_the_gbrowse_details_page



Other than looking at the code (available online at http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/cgi-bin/gbrowse_details), I don't know how to figure out how it infers things.


What specifically are you seeing that is inferred?  What does the relevant GFF3 look like?
Dave C.

On Thu, Aug 19, 2010 at 11:02 AM, Fariba M <fariba_mahdavifard at yahoo.com> wrote:


Hi Scott,

I have a question about Gbrowse, I would be grateful if you can help me.


The tutorial says that when we use a  "Link =
 AUTO" in [TRACK DEFAULTS] section,  an automatic link to a helper script named "gbrowse_details" will be generated.


I was wondering how this link is
 generated, because in the details page I can see info about gene sequences that are not even in my data file. I mean they are probably inferred from my data file, but I'd like to know how they are inferred. 

I'd like to know that, because I want to modify this details page a little bit and also use this inferred data as well. 

I think it should be possible to modify the details page, isn't it?


Thanks,Fariba







      
------------------------------------------------------------------------------

This SF.net email is sponsored by



Make an app they can't live without

Enter the BlackBerry Developer Challenge

http://p.sf.net/sfu/RIM-dev2dev 
_______________________________________________

Gmod-gbrowse mailing list

Gmod-gbrowse at lists.sourceforge.net

https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse





-- 
===> PLEASE KEEP RESPONSES ON THE LIST <===
http://gmod.org/wiki/GMOD_News
http://gmod.org/wiki/GMOD_Evo_Hackathon

http://gmod.org/wiki/GMOD_Europe_2010
http://gmod.org/wiki/Help_Desk_Feedback






------------------------------------------------------------------------------

Sell apps to millions through the Intel(R) Atom(Tm) Developer Program

Be part of this innovative community and reach millions of netbook users

worldwide. Take advantage of special opportunities to increase revenue and

speed time-to-market. Join now, and jumpstart your future.

http://p.sf.net/sfu/intel-atom-d2d
_______________________________________________

Gmod-gbrowse mailing list

Gmod-gbrowse at lists.sourceforge.net

https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse





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

Ontario Institute for Cancer Research




      
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://brie4.cshl.edu/pipermail/gmod-help/attachments/20100827/311c497b/attachment.html>