Hi Fariba,<br><br>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).<br>
<br>Scott<br><br><br><div class="gmail_quote">On Tue, Aug 24, 2010 at 7:25 PM, Dave Clements, GMOD Help Desk <span dir="ltr"><<a href="mailto:help@gmod.org">help@gmod.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi Fariba,<div><br></div><div>You can control some things on the gbrowse_details page using the methods listed at:</div><div><br></div><div><a href="http://gmod.org/wiki/GBrowse_Configuration_HOWTO#Controlling_the_gbrowse_details_page" target="_blank">http://gmod.org/wiki/GBrowse_Configuration_HOWTO#Controlling_the_gbrowse_details_page</a><br>
<br></div><div>Other than looking at the code (available online at <a href="http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/cgi-bin/gbrowse_details" target="_blank">http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/cgi-bin/gbrowse_details</a>), I don't know how to figure out how it infers things.</div>
<div><br></div><div>What specifically are you seeing that is inferred? What does the relevant GFF3 look like?</div><div><br></div><div>Dave C.</div><div><br></div><div><div class="gmail_quote"><div><div></div><div class="h5">
On Thu, Aug 19, 2010 at 11:02 AM, Fariba M <span dir="ltr"><<a href="mailto:fariba_mahdavifard@yahoo.com" target="_blank">fariba_mahdavifard@yahoo.com</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div class="h5"><table border="0" cellpadding="0" cellspacing="0">
<tbody><tr><td style="font: inherit;" valign="top"><span style="font-size: medium;"><font face="arial, helvetica, sans-serif">Hi Scott,</font></span><div>
<span style="font-size: medium;"><font face="arial, helvetica, sans-serif"><br></font></span></div><div><span style="font-size: medium;"><font face="arial, helvetica, sans-serif">I have a question about Gbrowse, I would be grateful if you can help me.</font></span></div>
<div><span style="font-size: medium;"><font face="arial, helvetica, sans-serif"><br></font></span></div><div><span style="font-size: medium;"><font face="arial, helvetica, sans-serif">The tutorial says that when we use a "Link =
AUTO</font></span><span style="font-size: medium;"><font face="arial, helvetica, sans-serif">" in </font></span><span style="white-space: pre-wrap;"><span style="font-size: medium;"><font face="arial, helvetica, sans-serif">[TRACK DEFAULTS] section,</font></span></span><span style="font-size: medium;"><font face="arial, helvetica, sans-serif"> an automatic link to a helper script named "gbrowse_details" will be generated.</font></span></div>
<div><span style="font-size: medium;"><font face="arial, helvetica, sans-serif"><br></font></span></div><div><span style="font-size: medium;"><font face="arial, helvetica, sans-serif">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. </font></span></div>
<div><span style="font-size: medium;"><font face="arial, helvetica, sans-serif">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. </font></span></div>
<div><span style="font-size: medium;"><font face="arial, helvetica, sans-serif">I think it should be possible to modify the details page, isn't it?</font></span></div><div><span style="font-size: medium;"><font face="arial, helvetica, sans-serif"><br>
</font></span></div><div><span style="font-size: medium;"><font face="arial, helvetica, sans-serif">Thanks,</font></span></div><div><span style="font-size: medium;"><font face="arial, helvetica, sans-serif">Fariba</font></span></div>
<div><div><span style="font-size: medium;"><font face="arial, helvetica, sans-serif"><br></font></span><div><br></div><div><br></div></div></div></td></tr></tbody></table><br>
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