GSQ_ATGDB.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);
?>

<div id='mainWLS' align="center">

<TABLE WIDTH="75%" CELLPADDING=3 CELLSPACING=3 ALIGN="center">
<TR>
<TD VALIGN=TOP>
<BR>
<H2 align="center">GeneSeqer@AtGDB - Guided Tutorial</H2>
<hr size=1 width="100%">

 <p>This step-by-step tutorial covers the basic concepts behind setting up and using the GeneSeqer@AtGDB web service.
We illustrate the individual steps necessary to use the <a HREF="http://www.plantgdb.org/cgi-bin/AtGeneSeqer.cgi">GeneSeqer@AtGDB</a> web service and tips 
to make its use more efficient and rewarding.</p>
 <BR>		
 <a HREF="#Setup"><font COLOR="#000000"><h3>Setting up GeneSeqer@AtGDB</h3></a></font>
 <ul>
 <li><a HREF="#Plan">Getting started</a></li>
 <li><a HREF="#EnterG">Step 1. Selecting genomic (target) sequence range</a></li>
 <li><a HREF="#EnterT">Step 2. Entering transcribed (query) sequence(s)</a></li>
 <li><a HREF="#Submit">Step 3. Submission</a></li>
 </ul>
 <a HREF="#Results"><font COLOR="#000000"><h3>Interpreting the results</h3></a></font>
 <ul>
 <li><a HREF="#Picture">The summary graphic</a></li>
 <li><a HREF="#Alignment">The alignment file</a></li>
 <li><a HREF="#Prediction">The predicted gene structures and ORFs</a></li>
 </ul>
 <a HREF="#MORE"><font COLOR="#000000"><h3>What's Next? </h3></a></font>
 <ul>
 <li><a HREF="#Homolog">Testing annotation results by homologous protein alignment</a></li>
 <li><a HREF="#Detailed">Submitting refined annotation </a></li>
 </ul>
<br>
<br>
<hr size=1 width="100%">

</tr>
</td>
</table>
 
<A name="Setup"></A>
<font color="#660033"><h3>Setting up GeneSeqer@AtGDB</h3></font>

<A name="Plan"></A>
<font color="#007766"><h4>Getting started</h4></font>
<P> The <a TARGET="_blank" HREF="http://www.plantgdb.org/cgi-bin/AtGeneSeqer.cgi">GeneSeqer@AtGDB</a> web service is intended primarily for the 
purpose of performing spliced alignment of query sequences (sequences representing transcribed genes, i.e. ESTs, cDNAs, 
and proteins) with a target region of the <I>Arabidopsis</I> genome. The results of such an alignment are useful in many studies. Because
there are a number of questions which may be addressed by spliced alignment, the process by which you use GeneSeqer@AtGDB may vary.
For instance, your choice of input sequence may be determined based on similarity to other sequences (both genomic and transcribed)
or you may wish to discover more about a specific gene region. In this example, the later case applies. The form
elements found in this tutorial are identical to those of the standard GeneSeqer@AtGDB web service. You may wish to 
<a TARGET="tutorial" HREF="http://www.plantgdb.org/cgi-bin/AtGeneSeqer.cgi">open GeneSeqer@AtGDB in a new window</a> and follow along in parallel
with this tutorial however this is not required.</P>
<BR>
<BR>

<A name="EnterG"></A>
<font color="#007766"><h4>Step 1. Selecting genomic (target) sequence range</h4></font>
<P> To demonstrate a typical use of this service, we have chosen to characterize a previously annotated segment of genomic sequence from 
<I>Arabdiopsis thaliana</I> (<a TARGET="_blank" HREF="http://www.plantgdb.org/cgi-bin/PlantGDB/GeneSeqer/AtGDBgs.cgi?ATchr=5&_a=24731000&_b=24741000">chromosome 5</a>).
This 10 kilobase (Kb) region of genomic sequence has been annotated as containing the gene models At5g625900 and At5g62600 in 
<A TARGET="_blank" HREF="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=nucleotide&list_uids=30698605">Version 4</A> of the
<I>Arabidopsis</I> Genome Initiative [AGI] chromosome annotation. Visualization of this region at 
<A TARGET="_blank" HREF="http://www.plantgdb.org/cgi-bin/PlantGDB/AtGDB/GCview.pl?chr=5&start=24731000&end=24741000">AtGDB</A> however, suggests that a single
gene occupies the region. GeneSeqer@AtGDB is used for further investigation.<BR><BR>
While the genomic segment in question could certainly be parsed from the whole chromosome sequence and then pasted into the standard
<A TARGET="_blank" HREF="http://www.plantgdb.org/cgi-bin/GeneSeqer.cgi">GeneSeqer@PlantGDB</A> service, a more direct route is provided by GeneSeqer@AtGDB
as shown below. For this example, simply selecting chromosome 5 and entering the region boundary is sufficient.<BR>
<B>TIP:</B> On every page of the AtGDB website the 'run GeneSeqer' and 'GeneSeqer@AtGDB' links will open a page to the GeneSeqer webservice and 
automatically select the chromosome and region corresponding to that which is currently being viewed. 
<BR>
<BR>
<TABLE width="50%" align="center">
 <TR><TD><TABLE width="50%" align="center">
  <TD align="left"><ul>
   <font COLOR="#FF0000">
   <li><h3>Select chromosome</h3></li>
   <li><h3>Enter appropriate range<BR>(ie. region boundary)</h3></li>
   </font>
  </ul></TD>
 </TABLE></TD></TR>
 <TD align="center">
  <hr />

<h2 align="center">STEP 1:&nbsp;&nbsp;&nbsp;&nbsp;Select Arabidopsis genomic DNA segment</h2><p />

<strong>Arabidopsis thaliana chromosome&nbsp;&nbsp</strong><input type="radio" name="ATchr" value="1" />1<input type="radio" name="ATchr" value="2" />2<input type="radio" name="ATchr" value="3" />3<input type="radio" name="ATchr" value="4" />4<input type="radio" name="ATchr" value="5" checked />5<br />

<a href="http://bioinformatics.iastate.edu/bioinformatics2go/gs/help.html#FROMTO">From position</a>: <input type="text" name="_a" value="25140563" size="10" />
<a href="http://bioinformatics.iastate.edu/bioinformatics2go/gs/help.html#FROMTO">to position</a>: <input type="text" name="_b" value="25149699" size="10" />

<a href="http://bioinformatics.iastate.edu/bioinformatics2go/gs/help.html#STRAND">Strand</a>: <input type="radio" name="_r" value="original " />original <input type="radio" name="_r" value="reverse " />reverse <input type="radio" name="_r" value="both" checked />both
<hr />
&nbsp;<p />


  <hr />
 </TD>
</TABLE>
</P>
<BR>
<BR>


<A name="EnterT"></A>
<font color="#007766"><h4>Step 2. Entering transcribed (query) sequence(s)</h4></font>
<P> In this situation an exhaustive alignment of "All Plant" ESTs and cDNAs is possible given the resonable size of our 
genomic sequence. Therefore these selections are chosen.<BR>
<BR>
The pre-gathered sequence collection choices (such as 'All Plants' and 'All Monocots') represent sequence groups made available
by <A TARGET="_blank" HREF="http://www.plantgdb.org">PlantGDB</A>. Feel free however to include your own sequences with which to
make alignments by entering them in the appropriate text boxes or uploading files containing them in FASTA format. A demonstration 
of this feature using homologous proteins aligned with our example region is shown <A HREF="#Homolog">below</A>.
<BR>
<BR>
<TABLE width="50%" align="center">
 <TR><TD><TABLE width="50%" align="center">
  <TD align="left"><ul>
   <font COLOR="#FF0000">
   <li><h3>Select "All Plants" EST & cDNA databases</h3></li>
   </font>
  </ul></TD>
 </TABLE></TD></TR>
 <TD align="center">
  <hr />

<h2 align="center">STEP 2:&nbsp;&nbsp;&nbsp;&nbsp;Select or input cDNA/EST sequences</h2><p />

Spliced Alignment: The output will show an optimal threading of a
         significantly matching cDNA/EST sequence into the genomic DNA by
         aligning putative exons only and displaying putative introns as
         (long) gaps in the cDNA/EST. You can supply your own EST/cDNA sequence as well as your own protein sequence to do the spliced alignment.
         However, your own EST/cDNA sequence can NOT be combined with our pre-processed databases (EST, TUG, or cDNA).<p />
<script language="javascript">
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<table cellpadding='4'>
<tr align="LEFT">
<th align="LEFT">Database</th>
<th align="LEFT">EST</th>

<th align="LEFT">TUG</th>
<th align="LEFT">cDNA</th>
<!-- <th align="LEFT">Protein</th> WAIT UNTIL GENESEQER2 TO ACTIVEATE THIS OPTION -->
</tr>
<tr align="LEFT">
<td><i>Shortcut</i></td>
</tr>

<tr>
<td><a href="http://www.zmdb.iastate.edu/PlantGDB/">All Plants</a></td>
<td><input type='checkbox' name='_d' value='AllPLANTest' checked></td>
<td><input type='checkbox' name='_d' value='AllPLANTtug'></td>
<td><input type='checkbox' name='_d' value='AllPLANTcdna' checked></td>
<!-- <td><input type='checkbox' name='_d' value='AllPLANTprotein'></td> WAIT UNTIL GENESEQER2 TO ACTIVEATE THIS OPTION -->
</tr>
<tr>

<td><a href="http://www.zmdb.iastate.edu/PlantGDB/">All Monocots</a></td>
<td><input type='checkbox' name='_d' value='AllMONOCOTest'></td>
<td><input type='checkbox' name='_d' value='AllMONOCOTtug'></td>
<td><input type='checkbox' name='_d' value='AllMONOCOTcdna'></td>
<!-- <td><input type='checkbox' name='_d' value='AllMONOCOTprotein'></td> WAIT UNTIL GENESEQER2 TO ACTIVEATE THIS OPTION -->
</tr>
<tr>
<td><a href="http://www.zmdb.iastate.edu/PlantGDB/">All Dicots</a></td>

<td><input type='checkbox' name='_d' value='AllDICOTest'></td>
<td><input type='checkbox' name='_d' value='AllDICOTtug'></td>
<td><input type='checkbox' name='_d' value='AllDICOTcdna'></td>
<!-- <td><input type='checkbox' name='_d' value='AllDICOTprotein'></td> WAIT UNTIL GENESEQER2 TO ACTIVEATE THIS OPTION -->
</tr>
<tr>
<td><a href="http://www.zmdb.iastate.edu/PlantGDB/">All Grasses</a></td>
<td><input type='checkbox' name='_d' value='AllGRASSest'></td>

<td><input type='checkbox' name='_d' value='AllGRASStug'></td>
<td><input type='checkbox' name='_d' value='AllGRASScdna'></td>
<!-- <td><input type='checkbox' name='_d' value='AllGRASSprotein'></td> WAIT UNTIL GENESEQER2 TO ACTIVEATE THIS OPTION -->
</tr>
<tr align='LEFT' id='activelink' style='display: none'>
<td colspan='4'><i><a href="#" onClick="toggleElement(hider_list); return false;">Click here to access the individual database for each species</a></i></td>
</tr>
<tr align='LEFT' id='inactivelink'>

<td><i>Individual species</i></td>
</tr>
<tr id='AT'>
<td><a target="_blank" href="http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=3702">Arabidopsis thaliana</a></td>
<td><input type='checkbox' name='_d' value='ATest'></td>
<td><input type='checkbox' name='_d' value='ATtug'></td>
<td><input type='checkbox' name='_d' value='ATcdna'></td>
<!-- <td><input type='checkbox' name='_d' value='ATprotein'></td> WAIT UNTIL GENESEQER2 TO ACTIVEATE THIS OPTION -->

</tr>
<tr id='AS'>
<td><a target="_blank" href="http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=4498">Avena sativa</a></td>
<td><input type='checkbox' name='_d' value='ASest'></td>
<td><input type='checkbox' name='_d' value='AStug'></td>
<td><input type='checkbox' name='_d' value='AScdna'></td>
<!-- <td><input type='checkbox' name='_d' value='ASprotein'></td> WAIT UNTIL GENESEQER2 TO ACTIVEATE THIS OPTION -->
</tr>

<tr id='BVSV'>
<td><a target="_blank" href="http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=3555">Beta vulgaris subsp. vulgaris</a></td>
<td><input type='checkbox' name='_d' value='BVSVest'></td>
<td><input type='checkbox' name='_d' value='BVSVtug'></td>
<td><input type='checkbox' name='_d' value='BVSVcdna'></td>
<!-- <td><input type='checkbox' name='_d' value='BVSVprotein'></td> WAIT UNTIL GENESEQER2 TO ACTIVEATE THISOPTION -->
</tr>
<tr id='GM'>

<td><a target="_blank" href="http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=3847">Glycine max</a></td>
<td><input type='checkbox' name='_d' value='GMest'></td>
<td><input type='checkbox' name='_d' value='GMtug'></td>
<td><input type='checkbox' name='_d' value='GMcdna'></td>
<!-- <td><input type='checkbox' name='_d' value='GMprotein'></td> WAIT UNTIL GENESEQER2 TO ACTIVEATE THIS OPTION -->
</tr>
<tr id='GA'>
<td><a target="_blank" href="http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=29729">Gossypium arboreum</a></td>

<td><input type='checkbox' name='_d' value='GAest'></td>
<td><input type='checkbox' name='_d' value='GAtug'></td>
<td><input type='checkbox' name='_d' value='GAcdna'></td>
<!-- <td><input type='checkbox' name='_d' value='GAprotein'></td> WAIT UNTIL GENESEQER2 TO ACTIVEATE THIS OPTION -->
</tr>
<tr id='GH'>
<td><a target="_blank" href="http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=3635">Gossypium hirsutum</a></td>
<td><input type='checkbox' name='_d' value='GHest'></td>

<td><input type='checkbox' name='_d' value='GHtug'></td>
<td><input type='checkbox' name='_d' value='GHcdna'></td>
<!-- <td><input type='checkbox' name='_d' value='GHprotein'></td> WAIT UNTIL GENESEQER2 TO ACTIVEATE THIS OPTION -->
</tr>
<tr id='HV'>
<td><a target="_blank" href="http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?mode=Info&amp;id=4513&amp;lvl=3&amp;nucl=1&amp;keep=1&amp;srchmode=1&amp;unlock">Hordeum vulgare</a></td>
<td><input type='checkbox' name='_d' value='HVest'></td>
<td><input type='checkbox' name='_d' value='HVtug'></td>

<td><input type='checkbox' name='_d' value='HVcdna'></td>
<!-- <td><input type='checkbox' name='_d' value='HVprotein'></td> WAIT UNTIL GENESEQER2 TO ACTIVEATE THIS OPTION -->
</tr>
<tr id='LJ'>
<td><a target="_blank" href="http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?mode=Info&amp;id=34305&amp;lvl=3&amp;nucl=1&amp;keep=1&amp;srchmode=1&amp;unlock">Lotus japonicus</a></td>
<td><input type='checkbox' name='_d' value='LJest'></td>
<td><input type='checkbox' name='_d' value='LJtug'></td>
<td><input type='checkbox' name='_d' value='LJcdna'></td>

<!-- <td><input type='checkbox' name='_d' value='LJprotein'></td> WAIT UNTIL GENESEQER2 TO ACTIVEATE THIS OPTION -->
</tr>
<tr id='LE'>
<td><a target="_blank" href="http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=4081">Lycopersicon esculentum</a></td>
<td><input type='checkbox' name='_d' value='LEest'></td>
<td><input type='checkbox' name='_d' value='LEtug'></td>
<td><input type='checkbox' name='_d' value='LEcdna'></td>
<!-- <td><input type='checkbox' name='_d' value='LEprotein'></td> WAIT UNTIL GENESEQER2 TO ACTIVEATE THIS OPTION -->

</tr>
<tr id='LH'>
<td><a target="_blank" href="http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=62890">Lycopersicon hirsutum</a></td>
<td><input type='checkbox' name='_d' value='LHest'></td>
<td><input type='checkbox' name='_d' value='LHtug'></td>
<td><input type='checkbox' name='_d' value='LHcdna'></td>
<!-- <td><input type='checkbox' name='_d' value='LHprotein'></td> WAIT UNTIL GENESEQER2 TO ACTIVEATE THIS OPTION -->
</tr>

<tr id='LP'>
<td><a target="_blank" href="http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=28526">Lycopersicon pennellii</a></td>
<td><input type='checkbox' name='_d' value='LPest'></td>
<td><input type='checkbox' name='_d' value='LPtug'></td>
<td><input type='checkbox' name='_d' value='LPcdna'></td>
<!-- <td><input type='checkbox' name='_d' value='LPprotein'></td> WAIT UNTIL GENESEQER2 TO ACTIVEATE THIS OPTION -->
</tr>
<tr id='MP'>

<td><a target="_blank" href="http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=3197">Marchantia polymorpha</a></td>
<td><input type='checkbox' name='_d' value='MPest'></td>
<td><input type='checkbox' name='_d' value='MPtug'></td>
<td><input type='checkbox' name='_d' value='MPcdna'></td>
<!-- <td><input type='checkbox' name='_d' value='MPprotein'></td> WAIT UNTIL GENESEQER2 TO ACTIVEATE THIS OPTION -->
</tr>
<tr id='MS'>
<td><a target="_blank" href="http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?mode=Info&amp;id=3879&amp;lvl=3&amp;nucl=1&amp;keep=1&amp;srchmode=1&amp;unlock">Medicago sativa</a></td>

<td><input type='checkbox' name='_d' value='MSest'></td>
<td><input type='checkbox' name='_d' value='MStug'></td>
<td><input type='checkbox' name='_d' value='MScdna'></td>
<!-- <td><input type='checkbox' name='_d' value='MSprotein'></td> WAIT UNTIL GENESEQER2 TO ACTIVEATE THIS OPTION -->
</tr>
<tr id='MT'>
<td><a target="_blank" href="http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=3880">Medicago truncatula</a></td>
<td><input type='checkbox' name='_d' value='MTest'></td>

<td><input type='checkbox' name='_d' value='MTtug'></td>
<td><input type='checkbox' name='_d' value='MTcdna'></td>
<!-- <td><input type='checkbox' name='_d' value='MTprotein'></td> WAIT UNTIL GENESEQER2 TO ACTIVEATE THIS OPTION -->
</tr>
<tr id='MC'>
<td><a target="_blank" href="http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=3554">Mesembryanthemum crystallinum</a></td>
<td><input type='checkbox' name='_d' value='MCest'></td>
<td><input type='checkbox' name='_d' value='MCtug'></td>

<td><input type='checkbox' name='_d' value='MCcdna'></td>
<!-- <td><input type='checkbox' name='_d' value='MCprotein'></td> WAIT UNTIL GENESEQER2 TO ACTIVEATE THIS OPTION -->
</tr>
<tr id='OS'>
<td><a target="_blank" href="http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=4530">Oryza sativa</a></td>
<td><input type='checkbox' name='_d' value='OSest'></td>
<td><input type='checkbox' name='_d' value='OStug'></td>
<td><input type='checkbox' name='_d' value='OScdna'></td>

<!-- <td><input type='checkbox' name='_d' value='OSprotein'></td> WAIT UNTIL GENESEQER2 TO ACTIVEATE THIS OPTION -->
</tr>
<tr id='PT'>
<td><a target="_blank" href="http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=3352">Pinus taeda</a></td>
<td><input type='checkbox' name='_d' value='PTest'></td>
<td><input type='checkbox' name='_d' value='PTtug'></td>
<td><input type='checkbox' name='_d' value='PTcdna'></td>
<!-- <td><input type='checkbox' name='_d' value='PTprotein'></td> WAIT UNTIL GENESEQER2 TO ACTIVEATE THIS OPTION -->

</tr>
<tr id='PTPT'>
<td><a target="_blank" href="http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=3352">Populus tremula X Populus tremuloides</a></td>
<td><input type='checkbox' name='_d' value='PTPTest'></td>
<td><input type='checkbox' name='_d' value='PTPTtug'></td>
<td><input type='checkbox' name='_d' value='PTPTcdna'></td>
<!-- <td><input type='checkbox' name='_d' value='PTPTprotein'></td> WAIT UNTIL GENESEQER2 TO ACTIVEATE THISOPTION -->
</tr>

<tr id='SC'>
<td><a target="_blank" href="http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?mode=Info&amp;id=4550&amp;lvl=3&amp;nucl=1&amp;keep=1&amp;srchmode=1&amp;unlock">Secale cereale</a></td>
<td><input type='checkbox' name='_d' value='SCest'></td>
<td><input type='checkbox' name='_d' value='SCtug'></td>
<td><input type='checkbox' name='_d' value='SCcdna'></td>
<!-- <td><input type='checkbox' name='_d' value='SCprotein'></td> WAIT UNTIL GENESEQER2 TO ACTIVEATE THIS OPTION -->
</tr>
<tr id='ST'>

<td><a target="_blank" href="http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?mode=Info&amp;id=4113&amp;lvl=3&amp;keep=1&amp;srchmode=1&amp;unlock">Solanum tuberosum</a></td>
<td><input type='checkbox' name='_d' value='STest'></td>
<td><input type='checkbox' name='_d' value='STtug'></td>
<td><input type='checkbox' name='_d' value='STcdna'></td>
<!-- <td><input type='checkbox' name='_d' value='STprotein'></td> WAIT UNTIL GENESEQER2 TO ACTIVEATE THIS OPTION -->
</tr>
<tr id='SB'>
<td><a target="_blank" href="http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=4558">Sorghum bicolor</a></td>

<td><input type='checkbox' name='_d' value='SBest'></td>
<td><input type='checkbox' name='_d' value='SBtug'></td>
<td><input type='checkbox' name='_d' value='SBcdna'></td>
<!-- <td><input type='checkbox' name='_d' value='SBprotein'></td> WAIT UNTIL GENESEQER2 TO ACTIVEATE THIS OPTION -->
</tr>
<tr id='SP'>
<td><a target="_blank" href="http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=132711">Sorghum propinquum</a></td>
<td><input type='checkbox' name='_d' value='SPest'></td>

<td><input type='checkbox' name='_d' value='SPtug'></td>
<td></td>
<!-- <td><input type='checkbox' name='_d' value='SPprotein'></td> WAIT UNTIL GENESEQER2 TO ACTIVEATE THIS OPTION -->
</tr>
<tr id='TA'>
<td><a target="_blank" href="http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?mode=Info&amp;id=4565&amp;lvl=3">Triticum aestivum</a></td>
<td><input type='checkbox' name='_d' value='TAest'></td>
<td><input type='checkbox' name='_d' value='TAtug'></td>

<td><input type='checkbox' name='_d' value='TAcdna'></td>
<!-- <td><input type='checkbox' name='_d' value='TAprotein'></td> WAIT UNTIL GENESEQER2 TO ACTIVEATE THIS OPTION -->
</tr>
<tr id='ZM'>
<td><a target="_blank" href="http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=4577">Zea mays</a></td>
<td><input type='checkbox' name='_d' value='ZMest'></td>
<td><input type='checkbox' name='_d' value='ZMtug'></td>
<td><input type='checkbox' name='_d' value='ZMcdna'></td>

<!-- <td><input type='checkbox' name='_d' value='ZMprotein'></td> WAIT UNTIL GENESEQER2 TO ACTIVEATE THIS OPTION -->
</tr>
</table>

<script language="javascript">
<!--

	if(document.getElementById || document.all)
		toggleElement(hider_list);

//-->
</script>

<table cellpadding='4'>
<tr><td><i>OR paste your own <b>EST/cDNA</b> sequence(s) here in <a HREF="http://bioinformatics.iastate.edu/bioinformatics2go/gs/help.html#FORMAT"> FASTA</a> format</i><br> <textarea name="_estp" rows=5 cols=60></textarea></td>

<td><i>... and/or paste your own <b>Protein</b> sequence(s) here in <a HREF="http://bioinformatics.iastate.edu/bioinformatics2go/gs/help.html#FORMAT"> FASTA</a> format</i><br> <textarea name="_trgpp" rows=5 cols=60></textarea></td>
</tr>
<tr><td><i>... and/or upload your <b>EST/cDNA</b> sequence file (specify file name):</i><br> <input type="file" name="_e"  size="60" /></td>

<td><i>... and/or upload your <b>Protein</b> sequence file (specify file name):</i><br> <input type="file" name="_q"  size="60" /></td>
</table>

  <hr />
 </TD>
</TABLE>
</P>
<BR>
<BR>


<A name="Submit"></A>
<font color="#007766"><h4>Step 3. Submission</h4></font>
<P> And finally our sequences are submitted. For a sequence such as this, analysis generally take only 10 min. For regions requiring
longer processing the results are available via email as well. The results of this demonstration have been cached and are therefore immediately 
available by clicking the submit button.<BR>
<B>TIP:</B> For large in-house analysis, the stand alone GeneSeqer application can be 
<A TARGET="_blank" HREF="http://bioinformatics.iastate.edu/bioinformatics2go/gs/download.html">downloaded here</A>
<BR>
<BR>
<TABLE width="50%" align="center">
 <TR><TD><TABLE width="50%" align="center">
  <TD align="left"><ul>
   <font COLOR="#FF0000">
   <li><h3>Submit for processing</h3></li>
   </font>
  </ul></TD>
 </TABLE></TD></TR>
 <TD align="center">
  <hr />

<h2 align="center">STEP 3:&nbsp;&nbsp;&nbsp;&nbsp;Submit job</h2><p />

Select "Submit" to send the job to the server. By default,
         output will be posted to your browser. You may select to have the
         ouput sent to you by email instead. Selection of this option is
         advised in the rare case that output posting is slow due to server
         overload.<p /><a NAME="SUBMITNOW"></a><input type="checkbox" name="Click" value="on" />Click here to send the output to this email address: <input type="text" name="email"  size="25" /><br /><input type="checkbox" name="HTML" value="on" />HTML formatted output [default: simple text].This option will not work if your mailer wraps long lines.<p />

<script LANGUAGE="JavaScript">
<!--
function showCachedResults(){
  window.location="#Results";
  window.open("./CHR5_GSQexample/At5GSQ.html","At5xGSQ");
return 0;
}

-->
</script>
<input type="button" value="Submit" onclick="showCachedResults();" />&nbsp; &nbsp; &nbsp;<input type="reset" />

<input type="hidden" name=".cgifields" value="_l" /><input type="hidden" name=".cgifields" value="Click" /><input type="hidden" name=".cgifields" value="HTML" /><input type="hidden" name=".cgifields" value="_r" /></form>

  <hr />
 </TD>
</TABLE>
</P>
<BR>
<BR>

<A name="Results"></A>
<font color="#660033"><h3>Interpreting the results</h3></font>
<P>If neccessary, click <a TARGET="At5xGSQ" HREF="./CHR5_GSQexample/At5GSQ.html">here</a> to open the results of the GeneSeqer@AtGDB 
analysis described above.<BR><BR><B>NOTE:</B> For large files, most browsers will take a while to correctly process all location tags. This may
cause links on the graphic to appear non-functional. After the browser has completely loaded the page however, all links will be fully
functional.</P>

<TABLE cellspacing=5>
<TD VALIGN="top"><BR><IMG SRC="./CHR5_GSQexample/At5_GSQdisplay.png" HSPACE=10></TD>
<TD ALIGN="left">
<A name="Picture" ></A>
<font color="#007766"><h4>The summary graphic</h4></font>
<P>Large genomic sequences are broken into fragments of 60000 bases for visualization. Each of these segments can be viewed by selecting
it in the drop down menu on the left of the results window. The corresponding graphic summary for each segment is displayed in the upper
pane of the results window. The summary graphic is clickable; by selecting a structure (colored arrow) within the graphic, the alignment file in
the lower pane will be scrolled to the appropriate section dealing with the element represented by your selection. Colored arrows represent
aligned sequences and predicted gene structures according to their unique color. In this example, red arrows represent predicted open 
reading frames; green arrows represent possible gene structures (possibly alternative structures); and blue arrows represent the alignment
of EST or cDNA sequences. For all arrow drawings exons are represented as colored rectangles connect by thin lines which depict introns.
A legend as to the color scheme is shown when you move your cursor over the "PREDICTION SUMMARY" title above the graphic.
</P>
<BR>

<A name="Alignment" ></A>
<font color="#007766"><h4>The alignment file</h4></font>
<P>The alignment file found in the lower pane of the results window is the heart of the GeneSeqer@AtGDB output. This text shows the 
base-to-base alignment of the expressed sequence(s) with the genomic DNA. Predicted introns are shown as strings of periods '.'.
Score statistics for the alignment quality as well as the predicted splice site quality are shown for each aligned sequence. In addition, 
links to the source of each sequence are provided above their respective alignments.</P>
</TD>
</TABLE>
<BR>
<A name="Prediction" ></A>
<font color="#007766"><h4>The predicted gene structures and ORFs</h4></font>
<P>The culmination of the GeneSeqer@AtGDB analysis is the prediction of an accurate gene structure. The quality of this prediction
can be assessed by prediction of a probable open reading frame (ORF) and comparison to know proteins. Predicted ORFs are shown as red
arrows in the summary graphic. Additionaly, the longest ORF as well as its translation frame is displayed in the alignment file. The
NCBI blastp link following the translated ORF sequence in the alignment file will allow you to more easily find putative homologs for this
putative gene. 
<BR>
<BR>
<BR>
<BR>

<A name="MORE" ></A>
<font color="#660033"><h3>What's Next? </h3></font>

<A name="Homolog" ></A>
<font color="#007766"><h4>Testing annotation results by homologous protein alignment</h4></font>
<BR>
<IMG ALIGN="center" SRC="./CHR5_GSQexample/At5protGSQ.png">
<P>Determining the complete gene structure, representing the entire coding region, of a gene is in some cases not possible using 
the alignment of transcribed sequences alone. As mentioned above, inclusion of homologous transcripts can 
increase the coverage of these alignments but is not always sufficient to produce a complete gene structure. For this reason, 
GeneSeqer@AtGDB includes the ability to align homologous proteins to your region of interest. These homologs may be determined through the use
of the NCBI blastp link provided in the ORF section of the web service results. The results shown 
<A TARGET="GSQxSBprot" HREF="./CHR5_GSQexample/At5protGSQ.html">here</A> represent such alignments with the chromosome 5
region of the <I>Arabidopsis thaliana</I> genome used throughout this demonstration.<BR>
<BR> 
The 8 putatively homologous proteins aligned in this example were obtained using the external BlastP link provided in the GeneSeqer@AtGDB text results.
Each ORF prediction found in the text results is followed by this link to facilitate searches against the NCBI non-redundant database.
In this example, all 8 proteins demonstrated e-values of at most 4e-54 and covered at least 900 of the 962 predicted amino acids of the longest ORF.
These 8 putatively homologous proteins were then downloaded from NCBI (in FASTA format). These sequences were subsequently used as query sequences 
in the GeneSeqer analysis referenced above by uploading this file of FASTA formated sequences in step 2 of the GeneSeqer@ATGDB job submission.
As was shown in the preceding section, homologous alignments of all 8 proteins suggests a single gene spanning this genomic region.
</P>
<BR> 
<BR> 


<A name="Detailed" ></A>
<font color="#007766"><h4>Submitting refined annotation</h4></font>
<BR>
<IMG ALIGN="center" SRC="./CHR5_GSQexample/At5_AtGDB.png">
<P>Static gene annotation, such as that provided for the <I>Arabidopsis thaliana</I> genome sequence, is inherently unreliable with respect to updated sequence
collections. In particular, matching ESTs, cDNAs, or proteins precisely supporting a given gene structure may not have been available at the time
the annotation was last frozen for submission. This problem, referred to as annotation lag is overcome only by dynamic assesment of gene annotation
in light of all current evidence. In order to facilitate collection of such assesments on a timely basis a User Contributed Annotation (UCA) service
has been established at AtGDB. Community contributed (and accessible) entry of annotation corrections (as demonstrated in this tutorial), weighted ranking of 
annotation accuracy, cross-referencing of static annotation versions corresponding to UCAs, and news forum style commentary on individual gene annotations
are among the project goals of the AtGDB UCA system. Instructions on how to contribute new annotations and annotation refinements such as the one described
herein are available at the main <A HREF="./index.php#UCA">AtGDB tutorial page</A>.
</P>
<BR>
<BR> 
<BR> 
<BR> 
</div>

<?php
require('SSI_GDBprep.php');
virtual("${CGIPATH}SSI_GDBgui.pl/STANDARD_FOOTER/" . $SSI_QUERYSTRING);
?>
See more files for this project here