index.php from eXtensible Genome Data Broker at Krugle

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<?php
if(empty($SITEDEF_H)){require('SITEDEF.php');}
if(empty($PARAM_H)){require('getPARAM.php');}
require('SSI_GDBprep.php');
virtual("${CGIPATH}SSI_GDBgui.pl/TWO_COLUMN_HEADER/" . $SSI_QUERYSTRING);
?>

<STYLE TYPE="text/css">
h3.UCA { 
 padding:1px 5px; margin:2px;
 border:1px solid maroon; background:#336666;
 color:#FFFFFF; font:bold 100% stencil,cursive;
}
#showcase { 
width:615px; text-align:justify; float:left;
margin-right:15px; margin-bottom:15px;
border-color:#999966; border-style:solid; border-width:thin;
}
#SCtitle {
background-color:#999966;padding-left:25;
color:lightgrey;
}
</STYLE>

<div align="left">

<h2 align="center"><font color="#000000"><big>Community Annotation</big></font></h2>

<P style="margin-right:32px; text-align:left;">Annotation of genes within the <I>Arabidopsis thaliana</I> genome is 
a dynamic challenge in which the depth of the current EST and cDNA collections and
the state of the genomic sequence assembly dictate the quality of each predicted gene 
model. At AtGDB, acknowledgement and correction of gene models (some of which may have
been improperly annotated in the current genome assembly) is made possible through the
use of <B>User Contributed Annotations</B>.
</P>

<table ID='showcase'>
<tr>
 <td id='SCtitle' COLSPAN=2 >UCA SHOWCASE</td>
</tr>
<tr>
 <td> 
   <table style="border-color:#000000;border-style:solid;border-width:thin;" >
     <tr><td><IMG SRC='Showcase/04mar11/ruler.png'></td></tr>
     <tr><td><IMG SRC='Showcase/04mar11/UCA.png'></td></tr>
     <tr><td><IMG SRC='Showcase/04mar11/GBK.png'></td></tr>
     <tr><td><IMG SRC='Showcase/04mar11/CDNA.png'></td></tr>
     <tr><td><IMG SRC='Showcase/04mar11/EST.png'></td></tr>
   </table>
 </td>
</tr>
<tr>
 <td valign='TOP'>
   <P>
   <A HREF=<?php echo "'${CGIPATH}getRegion.pl?dbid=0&chr=2&l_pos=17603963&r_pos=17606215'"; ?>><B>UCA-At2g42245:</B></A><BR>
The User Contributed Annotation (green gene structure) to the left shows how a user of AtGDB 
has provided an updated annotation. This annotation explains the inconsistancy of the current
gene models with the spliced alignment of ESTs and cDNAs in this region.
   </P>   
 </td>
</tr>
</table>

<DIV style='margin-left:800px; width:300px;'>
<h3 class="UCA" style='clear:right; white-space:nowrap;'><U>G</U>enome <U>A</U>nnotation <U>EVAL</U>uation</h3>
<P style='margin-top:2px;'>
A key design feature of the AtGDB UCA system is that potentially erroneous gene structure
models in the current annotation are flagged, and cDNA and EST evidence is provided on-line
in conjunction with analysis tools. Using these automated flags, in many cases,will allow users to quickly
and confidently provide corrected gene models. 
</P>
<UL>
<LI><A HREF='./gaeval/'>GAEVAL technical description</A></LI>
<LI><A HREF='./gaeval/gaeval_lists.php'>Lists of problematic gene models</A></LI>
</UL>

<h3 class="UCA" >Tutorials</h3>
<UL>
<LI><a HREF='/AtGDB/tutorial/UCA_ATGDB.php'>Submitting a User Contributed Annotation?</a></LI>
<LI><A HREF='/AtGDB/tutorial/HOWTO/GSannotation/index.php'>Annotating Gene Structure using GeneSeqer?</A></LI>
</UL>

<h3 class="UCA" >UCA statistics & resources</h3>
<UL>
<LI><a HREF='./UCAlist.php'>Contributed Annotations</a></LI>
<LI><A HREF='/AtGDB/Interns/'>Internships & Outreach</A></LI>
</UL>

</DIV>
</div>

<?php
require('SSI_GDBprep.php');
virtual("${CGIPATH}SSI_GDBgui.pl/STANDARD_FOOTER/" . $SSI_QUERYSTRING);
?>

See more files for this project here

eXtensible Genome Data Broker

The xGDB project provides scientists with an online portal for the integration of diverse sources of genomic data. Portals allow researchers to effectively target a specific scientific question by customizing their interactions with available data.

Project homepage: http://sourceforge.net/projects/xgdb
Programming language(s): JavaScript,Perl,PHP
License: other

  Showcase/
    03nov01/
      CDNA.png
      EST.png
      GBK.png
      UCA.png
      description.html
      ruler.png
    04mar11/
      CDNA.png
      EST.png
      GBK.png
      UCA.png
      description.html
      ruler.png
    GeneModelMerge/
      CDNA.png
      EST.png
      GBK.png
      UCA.png
      index.php
      ruler.png
    GeneModelSplit/
      CDNA.png
      EST.png
      GBK.png
      UCA.png
      index.php
      ruler.png
  gaeval/
    examples/
      altspl.png
      amb3.png
      amb5.png
      att.png
      cov0.png
      cov1.png
      cov2.png
      cov3.png
      cov4.png
      fission.png
      fussion.png
      ovext.png
      unext.png
    GLquery.css
    GLquery.js
    cps.php
    fig1.png
    fig2.png
    figa.png
    gaeval_lists.php
    index.php
  ATchr2.aln
  ATchr3.aln
  ATchr5.aln
  UCAlist.php
  index.php
  vector.php