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walkthrough.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">

<FORM METHOD="POST" NAME="gsFORM">

<CENTER>
<TABLE>
<TR><TD><A HREF="http://www.plantgdb.org/cgi-bin/PlantGDB/GeneSeqer/PlantGDBgs.cgi"><IMG SRC="sleuth1.JPG" WIDTH=101 HEIGHT=121 ALIGN=left></A>
</TD><TD align='center'><P><FONT SIZE="+3" COLOR="#009900"><B>AtGDB Gene Structure Annotation: HOW-TO</B></FONT><BR>
As you progress, you may find some of the
information or instructions confusing.<BR> At any time you may click
<A HREF="terms_and_concepts.htm" TARGET="_blank">here</FONT></A>
to go back and review the vocabulary.
</P></TD>
</TABLE>
</CENTER>

<P>&nbsp;</P>

<P><FONT SIZE="+2" COLOR="#009900">STEP&nbsp;1: Finding a
DNA&nbsp;sequence</FONT><FONT SIZE="+1" COLOR="#009900">.</FONT></P>

<BLOCKQUOTE>In order to begin using this service you must first have
   a DNA&nbsp;sequence. Now, if you are a researcher you would be
   discovering your own DNA&nbsp;sequences that you are interested
   in. However, since most using this site are not current
   researchers, someone who IS&nbsp;currently doing research has
   provided a list of DNA&nbsp;sequences that they are interested in
   and that they think may prove to be interesting. Say 'thank
   you'&nbsp;to Dr. Volker Brendel's research group at Iowa State
   University. 
   
   <P>When choosing a sequence it is important to choose sequences of
   less than about 30,000 base pairs. The GeneSeqer program will take
   roughly one half hour to perform a search on a sequence of about
   60,000 base pairs. Use this as a guide so that your search can be
   done in a timely manner. Please choose a DNA&nbsp;sequence from
   the drop down list of sequences below to run on the GeneSeqer
   program.</P></BLOCKQUOTE>


<CENTER>
<?php
  if(empty($SITEDEF_H)){require('/ZMDB/home/httpd/html/PlantGDB/AtGDB/phplib/ATGDB_SITEDEF.php');}

//   echo "VALUES FROM HTTP_POST_VARS<BR>";
//   while($element = each($HTTP_POST_VARS)){
//     echo $element["key"] . " - " . $element["value"] . "<BR>\n";
//   }
//   echo "VALUES FROM HTTP_GET_VARS<BR>";
//   while($element = each($HTTP_GET_VARS)){
//     echo $element["key"] . " - " . $element["value"] . "<BR>\n";
//   }

// Default GSQ@AtGDB webservice
  $GSQwebservice = "http://www.plantgdb.org/cgi-bin/PlantGDB/GeneSeqer/AtGDBgs.cgi";
  $allEST  = "CHECKED";
  $allTUG  = "";
  $allCDNA = "CHECKED";

  if(($HTTP_POST_VARS["NovelSeq"])&&($HTTP_POST_VARS["NovelSeq"] != "Choose an unknown gene")){

    $retValues = explode(":",$HTTP_POST_VARS["NovelSeq"]);

    $lpos = $retValues[3] - 500;
    $rpos = $retValues[4] + 500;
    if($retValues[2] == 1){
      $gbACC = "NC_003070";
      $chr = 1;
    }elseif($retValues[2] == 2){
      $gbACC = "NC_003071";
      $chr = 2;
    }elseif($retValues[2] == 3){
      $gbACC = "NC_003074";
      $chr = 3;
    }elseif($retValues[2] == 4){
      $gbACC = "NC_003075";
      $chr = 4;
    }elseif($retValues[2] == 5){
      $gbACC = "NC_003076";
      $chr = 5;
    }

    echo "<INPUT TYPE='hidden' NAME=ATchr VALUE='$chr'>\n";
    echo "You have selected a region in which unknown (never before annotated) genes may be found<BR>\n";
    echo "To select another gene <A HREF='./walkthrough.php'>click here</A><BR>\n";
    echo "<P ALIGN='LEFT'>To view this gene region <A HREF='${CGIPATH}GCview.pl?chr=$chr&start=$lpos&end=$rpos' TARGET='_blank'>click here</A><BR>\n";
    echo "<B>STEP 1:</B> Selected Gene = <B>NOVEL</B><BR>\n";
    echo "<B>STEP 2:</B> Genomic Region = <I>Arabidopsis thaliana</I> chromosome $chr bases $lpos to $rpos<BR>\n";
    echo "<B>STEP 3:</B> cDNA/EST selection = 'All Plant EST' and 'All Plant cDNA'<BR>\n";
    echo "<B>STEP 4:</B> Splice site model = Arabidopsis<BR>\n";
    echo "<B>STEP 5:</B> Review the supplied entries in Steps 1-4 and then continue to step 5 for submission<BR>\n";

  }elseif(($HTTP_POST_VARS["ShortSeq"])&&($HTTP_POST_VARS["ShortSeq"] != "Choose a gene to SHORTEN")){

    $retValues = explode(":",$HTTP_POST_VARS["ShortSeq"]);

    $lpos = $retValues[3] - 500;
    $rpos = $retValues[4] + 500;
    if($retValues[2] == 1){
      $gbACC = "NC_003070";
      $chr = 1;
    }elseif($retValues[2] == 2){
      $gbACC = "NC_003071";
      $chr = 2;
    }elseif($retValues[2] == 3){
      $gbACC = "NC_003074";
      $chr = 3;
    }elseif($retValues[2] == 4){
      $gbACC = "NC_003075";
      $chr = 4;
    }elseif($retValues[2] == 5){
      $gbACC = "NC_003076";
      $chr = 5;
    }

    echo "<INPUT TYPE='hidden' NAME=ATchr VALUE='$chr'>\n";
    echo "You have selected the gene <B>$retValues[1]</B> which may need to be shortened<BR>\n";
    echo "To select another gene <A HREF='./walkthrough.php'>click here</A><BR>\n";
    echo "<P ALIGN='LEFT'>To view this gene <A HREF='${CGIPATH}GCfind.pl?searchSTR=$retValues[1]' TARGET='_blank'>click here</A><BR>\n";
    echo "<B>STEP 1:</B> Selected Gene = $retValues[1]<BR>\n";
    echo "<B>STEP 2:</B> Genomic Region = <I>Arabidopsis thaliana</I> chromosome $chr bases $lpos to $rpos<BR>\n";
    echo "<B>STEP 3:</B> cDNA/EST selection = 'All Plant EST' and 'All Plant cDNA'<BR>\n";
    echo "<B>STEP 4:</B> Splice site model = Arabidopsis<BR>\n";
    echo "<B>STEP 5:</B> Review the supplied entries in Steps 1-4 and then continue to step 5 for submission<BR>\n";

  }elseif(($HTTP_POST_VARS["SplitSeq"])&&($HTTP_POST_VARS["SplitSeq"] != "Choose a gene to SPLIT")){

    $retValues = explode(":",$HTTP_POST_VARS["SplitSeq"]);

    $lpos = $retValues[3] - 500;
    $rpos = $retValues[4] + 500;
    if($retValues[2] == 1){
      $gbACC = "NC_003070";
      $chr = 1;
    }elseif($retValues[2] == 2){
      $gbACC = "NC_003071";
      $chr = 2;
    }elseif($retValues[2] == 3){
      $gbACC = "NC_003074";
      $chr = 3;
    }elseif($retValues[2] == 4){
      $gbACC = "NC_003075";
      $chr = 4;
    }elseif($retValues[2] == 5){
      $gbACC = "NC_003076";
      $chr = 5;
    }

    echo "<INPUT TYPE='hidden' NAME=ATchr VALUE='$chr'>\n";
    echo "You have selected the gene <B>$retValues[1]</B> which may need to be split into multiple gene annotations<BR>\n";
    echo "To select another gene <A HREF='./walkthrough.php'>click here</A><BR>\n";
    echo "<P ALIGN='LEFT'>To view this gene <A HREF='${CGIPATH}GCfind.pl?searchSTR=$retValues[1]' TARGET='_blank'>click here</A><BR>\n";
    echo "<B>STEP 1:</B> Selected Gene = $retValues[1]<BR>\n";
    echo "<B>STEP 2:</B> Genomic Region = <I>Arabidopsis thaliana</I> chromosome $chr bases $lpos to $rpos<BR>\n";
    echo "<B>STEP 3:</B> cDNA/EST selection = 'All Plant EST' and 'All Plant cDNA'<BR>\n";
    echo "<B>STEP 4:</B> Splice site model = Arabidopsis<BR>\n";
    echo "<B>STEP 5:</B> Review the supplied entries in Steps 1-4 and then continue to step 5 for submission<BR>\n";

  }elseif(($HTTP_POST_VARS["AltSeq"])&&($HTTP_POST_VARS["AltSeq"] != "Choose a gene with ALTERNATIVE STRUCTURE")){

    $retValues = explode(":",$HTTP_POST_VARS["AltSeq"]);

    $lpos = $retValues[3] - 500;
    $rpos = $retValues[4] + 500;
    if($retValues[2] == 1){
      $gbACC = "NC_003070";
      $chr = 1;
    }elseif($retValues[2] == 2){
      $gbACC = "NC_003071";
      $chr = 2;
    }elseif($retValues[2] == 3){
      $gbACC = "NC_003074";
      $chr = 3;
    }elseif($retValues[2] == 4){
      $gbACC = "NC_003075";
      $chr = 4;
    }elseif($retValues[2] == 5){
      $gbACC = "NC_003076";
      $chr = 5;
    }

    echo "<INPUT TYPE='hidden' NAME=ATchr VALUE='$chr'>\n";
    echo "You have selected the gene <B>$retValues[1]</B> which may have an UNREPRESENTED alternative structure<BR>\n";
    echo "To select another gene <A HREF='./walkthrough.php'>click here</A><BR>\n";
    echo "<P ALIGN='LEFT'>To view this gene <A HREF='${CGIPATH}GCfind.pl?searchSTR=$retValues[1]' TARGET='_blank'>click here</A><BR>\n";
    echo "<B>STEP 1:</B> Selected Gene = $retValues[1]<BR>\n";
    echo "<B>STEP 2:</B> Genomic Region = <I>Arabidopsis thaliana</I> chromosome $chr bases $lpos to $rpos<BR>\n";
    echo "<B>STEP 3:</B> cDNA/EST selection = 'All Plant EST' and 'All Plant cDNA'<BR>\n";
    echo "<B>STEP 4:</B> Splice site model = Arabidopsis<BR>\n";
    echo "<B>STEP 5:</B> Review the supplied entries in Steps 1-4 and then continue to step 5 for submission<BR>\n";

  }elseif(($HTTP_POST_VARS["ExtSeq"])&&($HTTP_POST_VARS["ExtSeq"] != "Choose a gene to EXTEND")){

    $retValues = explode(":",$HTTP_POST_VARS["ExtSeq"]);

    $lpos = $retValues[3] - 500;
    $rpos = $retValues[4] + 500;
    if($retValues[2] == 1){
      $gbACC = "NC_003070";
      $chr = 1;
    }elseif($retValues[2] == 2){
      $gbACC = "NC_003071";
      $chr = 2;
    }elseif($retValues[2] == 3){
      $gbACC = "NC_003074";
      $chr = 3;
    }elseif($retValues[2] == 4){
      $gbACC = "NC_003075";
      $chr = 4;
    }elseif($retValues[2] == 5){
      $gbACC = "NC_003076";
      $chr = 5;
    }

    echo "<INPUT TYPE='hidden' NAME=ATchr VALUE='$chr'>\n";
    echo "You have selected the gene <B>$retValues[1]</B> which may need to be extended<BR>\n";
    echo "To select another gene <A HREF='./walkthrough.php'>click here</A><BR>\n";
    echo "<P ALIGN='LEFT'>To view this gene <A HREF='${CGIPATH}GCfind.pl?searchSTR=$retValues[1]' TARGET='_blank'>click here</A><BR>\n";
    echo "<B>STEP 1:</B> Selected Gene = $retValues[1]<BR>\n";
    echo "<B>STEP 2:</B> Genomic Region = <I>Arabidopsis thaliana</I> chromosome $chr bases $lpos to $rpos<BR>\n";
    echo "<B>STEP 3:</B> cDNA/EST selection = 'All Plant EST' and 'All Plant cDNA'<BR>\n";
    echo "<B>STEP 4:</B> Splice site model = Arabidopsis<BR>\n";
    echo "<B>STEP 5:</B> Review the supplied entries in Steps 1-4 and then continue to step 5 for submission<BR>\n";

  }elseif(($HTTP_POST_VARS["MergeSeq"])&&($HTTP_POST_VARS["MergeSeq"] != "Choose a gene pair to MERGE")){

    $retValues = explode("&",$HTTP_POST_VARS["MergeSeq"]);
    $retValues_G1 = explode(":",$retValues[0]);
    $retValues_G2 = explode(":",$retValues[1]);

    if($retValues_G1[3] <= $retValues_G2[3]){
      $lpos = $retValues_G1[3] - 500;
    }else{
      $lpos = $retValues_G2[3] - 500;
    }

    if($retValues_G1[4] >= $retValues_G2[4]){
      $rpos = $retValues_G1[4] + 500;
    }else{ 
      $rpos = $retValues_G2[4] + 500;
    }

    if($retValues_G1[2] == 1){
      $gbACC = "NC_003070";
      $chr = 1;
    }elseif($retValues_G1[2] == 2){
      $gbACC = "NC_003071";
      $chr = 2;
    }elseif($retValues_G1[2] == 3){
      $gbACC = "NC_003074";
      $chr = 3;
    }elseif($retValues_G1[2] == 4){
      $gbACC = "NC_003075";
      $chr = 4;
    }elseif($retValues_G1[2] == 5){
      $gbACC = "NC_003076";
      $chr = 5;
    }

    echo "<INPUT TYPE='hidden' NAME=ATchr VALUE='$chr'>\n";
    echo "You have selected the gene pair $retValues_G1[1] -- $retValues_G2[1] which may need to be merged into a single gene annotation<BR>\n";
    echo "To select another gene <A HREF='./walkthrough.php'>click here</A><BR>\n";
    echo "<P ALIGN='LEFT'>To view this gene region <A HREF='${CGIPATH}GCview.pl?chr=$chr&start=$lpos&end=$rpos' TARGET='_blank'>click here</A><BR>\n";
    echo "<B>STEP 1:</B> Selected Gene Pair = $retValues_G1[1] -- $retValues_G2[1]<BR>\n";
    echo "<B>STEP 2:</B> Genomic Region = <I>Arabidopsis thaliana</I> chromosome $retValues_G1[2] bases $lpos to $rpos<BR>\n";
    echo "<B>STEP 3:</B> cDNA/EST selection = 'All Plant EST' and 'All Plant cDNA'<BR>\n";
    echo "<B>STEP 4:</B> Splice site model = Arabidopsis<BR>\n";
    echo "<B>STEP 5:</B> Review the supplied entries in Steps 1-4 and then continue to step 5 for submission<BR>\n";

  }else{
    // Set up default form values
    $lpos  = "";
    $rpos  = "";
    $gbACC = "";
    $GSQwebservice = "http://www.plantgdb.org/cgi-bin/PlantGDB/GeneSeqer/PlantGDBgs.cgi";
    $allEST  = "";
    $allTUG  = "CHECKED";
    $allCDNA = "";

    // Query ATGDB database for annotation error lists
    $dbh = mysql_connect($DB_HOST,$DB_USER,$DB_PASSWORD);
    mysql_select_db(end($DB));

    echo "<INPUT TYPE=Button NAME=RandSeq ONCLICK=\"randomSubmit();\" VALUE=\"Give me a Sequence -- Any Sequence\"><BR><BR><NOBR>\n";
    echo "<SELECT NAME=NovelSeq ONCHANGE='submit();'>\n<OPTION SELECTED>Choose an unknown gene</OPTION>\n";

    echo "</SELECT>\n";
    echo "<SELECT NAME=ShortSeq ONCHANGE='submit();'>\n<OPTION SELECTED>Choose a gene to SHORTEN</OPTION>\n";

    $sth = mysql_query("SELECT DISTINCT g.uid,g.geneId,g.chr,g.l_pos,g.r_pos,a.utr5stat,a.utr3stat,a.user_annotated_geneId from gbk_gene_annotation as g,gbk_gaeval as a where (g.uid = a.uid) && ((a.utr5stat = 1)||(a.utr3stat = 1)||((a.props RLIKE '[[:<:]]12[[:>:]]')&&(a.utr5stat = 2))||((a.props RLIKE '[[:<:]]22[[:>:]]')&&(a.utr3stat = 2))) ORDER BY g.geneId");

    if($HTTP_POST_VARS["ShowALL"]){
      while( $row = mysql_fetch_row($sth)){
        if(($row[5] == 1)||($row[6] == 1)){
          $AMB = " A";
        }else{
          $AMB = "";
        }
        if($row[7]){
          echo "<OPTION VALUE='$row[0]:$row[1]:$row[2]:$row[3]:$row[4]:$row[5]:$row[6]' style=\"color:#0000FF\">$row[1] $AMB</OPTION>\n";
        }else{
          echo "<OPTION VALUE='$row[0]:$row[1]:$row[2]:$row[3]:$row[4]:$row[5]:$row[6]'>$row[1] $AMB</OPTION>\n";
        }
      }
    }else{
      $num_results = mysql_num_rows($sth);
      $magic_num = 0; $row_num = 0; $returned_results = 1;

      while( $row = mysql_fetch_row($sth)){
        if($row_num == $magic_num){
          // set the next magic_num
          $returned_results++;
          if($returned_results < 20){
            $magic_num = rand($magic_num + 1,( $num_results/20 * $returned_results ));
          }elseif($returned_results > 20){
            $magic_num = -1;
          }else{
            $magic_num = rand($magic_num + 1,$num_results);
          }

          // print the magic row
          if(($row[5] == 1)||($row[6] == 1)){
            $AMB = " A";
          }else{
            $AMB = "";
          }
          if($row[7]){
            echo "<OPTION VALUE='$row[0]:$row[1]:$row[2]:$row[3]:$row[4]:$row[5]:$row[6]' style=\"color:#0000FF\">$row[1] $AMB</OPTION>\n";
          }else{
            echo "<OPTION VALUE='$row[0]:$row[1]:$row[2]:$row[3]:$row[4]:$row[5]:$row[6]'>$row[1] $AMB</OPTION>\n";
          }
        }
        $row_num++;
      }
    }
    echo "</SELECT>\n";
    echo "<SELECT NAME=SplitSeq ONCHANGE='submit();'>\n<OPTION SELECTED>Choose a gene to SPLIT</OPTION>\n";

    $sth = mysql_query("SELECT DISTINCT g.uid,g.geneId,g.chr,g.l_pos,g.r_pos,a.user_annotated_geneId from gbk_gene_annotation as g,gbk_gaeval as a where (g.uid = a.uid) && (a.props RLIKE '[[:<:]]1[[:>:]]') ORDER BY g.geneId");

    if($HTTP_POST_VARS["ShowALL"]){
      while( $row = mysql_fetch_row($sth)){
        if($row[5]){
          echo "<OPTION VALUE='$row[0]:$row[1]:$row[2]:$row[3]:$row[4]' style=\"color:#0000FF\">$row[1]</OPTION>\n";
        }else{
          echo "<OPTION VALUE='$row[0]:$row[1]:$row[2]:$row[3]:$row[4]'>$row[1]</OPTION>\n";
        }
      }
    }else{
      $num_results = mysql_num_rows($sth);
      $magic_num = 0; $row_num = 0; $returned_results = 1;
  
      while( $row = mysql_fetch_row($sth)){
        if($row_num == $magic_num){
          // set the next magic_num
          $returned_results++;
          if($returned_results < 20){
            $magic_num = rand($magic_num + 1,( $num_results/20 * $returned_results ));
          }elseif($returned_results > 20){
            $magic_num = -1;
          }else{
            $magic_num = rand($magic_num + 1,$num_results);
          }
  
          // print the magic row
          if($row[5]){
            echo "<OPTION VALUE='$row[0]:$row[1]:$row[2]:$row[3]:$row[4]' style=\"color:#0000FF\">$row[1]</OPTION>\n";
          }else{
            echo "<OPTION VALUE='$row[0]:$row[1]:$row[2]:$row[3]:$row[4]'>$row[1]</OPTION>\n";
          }
        }
        $row_num++;
      }
    }
    echo "</SELECT>\n";
    echo "<BR>\n";
    echo "<SELECT NAME=AltSeq ONCHANGE='submit();'>\n<OPTION SELECTED>Choose a gene with ALTERNATIVE STRUCTURE</OPTION>\n";

    $sth = mysql_query("SELECT DISTINCT g.uid,g.geneId,g.chr,g.l_pos,g.r_pos,a.user_annotated_geneId from gbk_gene_annotation as g,gbk_gaeval as a where (g.uid = a.uid) && (a.props RLIKE '[[:<:]]3[[:>:]]') ORDER BY g.geneId");

    if($HTTP_POST_VARS["ShowALL"]){
      while( $row = mysql_fetch_row($sth)){
        if($row[5]){
          echo "<OPTION VALUE='$row[0]:$row[1]:$row[2]:$row[3]:$row[4]' style=\"color:#0000FF\">$row[1]</OPTION>\n";
        }else{
          echo "<OPTION VALUE='$row[0]:$row[1]:$row[2]:$row[3]:$row[4]'>$row[1]</OPTION>\n";
        }
      }
    }else{
      $num_results = mysql_num_rows($sth);
      $magic_num = 0; $row_num = 0; $returned_results = 1;
  
      while( $row = mysql_fetch_row($sth)){
        if($row_num == $magic_num){
          // set the next magic_num
          $returned_results++;
          if($returned_results < 20){
            $magic_num = rand($magic_num + 1,( $num_results/20 * $returned_results ));
          }elseif($returned_results > 20){
            $magic_num = -1;
          }else{
            $magic_num = rand($magic_num + 1,$num_results);
          }
  
          // print the magic row
          if($row[5]){
            echo "<OPTION VALUE='$row[0]:$row[1]:$row[2]:$row[3]:$row[4]' style=\"color:#0000FF\">$row[1]</OPTION>\n";
          }else{
            echo "<OPTION VALUE='$row[0]:$row[1]:$row[2]:$row[3]:$row[4]'>$row[1]</OPTION>\n";
          }
        }
        $row_num++;
      }
    }
    echo "</SELECT>\n";
    echo "<SELECT NAME=ExtSeq ONCHANGE='submit();'>\n<OPTION SELECTED>Choose a gene to EXTEND</OPTION>\n";

    $sth = mysql_query("SELECT DISTINCT g.uid,g.geneId,g.chr,g.l_pos,g.r_pos,a.user_annotated_geneId from gbk_gene_annotation as g,gbk_gaeval as a where (g.uid = a.uid) && (((a.props RLIKE '[[:<:]]13[[:>:]]')&&(a.utr5stat = 3))||((a.props RLIKE '[[:<:]]23[[:>:]]')&&(a.utr5stat = 3))) ORDER BY g.geneId");

    if($HTTP_POST_VARS["ShowALL"]){
      while( $row = mysql_fetch_row($sth)){
        if($row[5]){
          echo "<OPTION VALUE='$row[0]:$row[1]:$row[2]:$row[3]:$row[4]' style=\"color:#0000FF\">$row[1]</OPTION>\n";
        }else{
          echo "<OPTION VALUE='$row[0]:$row[1]:$row[2]:$row[3]:$row[4]'>$row[1]</OPTION>\n";
        }
      }
    }else{
      $num_results = mysql_num_rows($sth);
      $magic_num = 0; $row_num = 0; $returned_results = 1;
  
      while( $row = mysql_fetch_row($sth)){
         if($row_num == $magic_num){
          // set the next magic_num
          $returned_results++;
          if($returned_results < 20){
            $magic_num = rand($magic_num + 1,( $num_results/20 * $returned_results ));
          }elseif($returned_results > 20){
            $magic_num = -1;
          }else{
            $magic_num = rand($magic_num + 1,$num_results);
          }

          // print the magic row
          if($row[5]){
            echo "<OPTION VALUE='$row[0]:$row[1]:$row[2]:$row[3]:$row[4]' style=\"color:#0000FF\">$row[1]</OPTION>\n";
          }else{
            echo "<OPTION VALUE='$row[0]:$row[1]:$row[2]:$row[3]:$row[4]'>$row[1]</OPTION>\n";
          }
        }
        $row_num++;
      }
    }
    echo "</SELECT>\n";
    echo "<SELECT NAME=MergeSeq ONCHANGE='submit();'>\n<OPTION SELECTED>Choose a gene pair to MERGE</OPTION>\n";

    $PREV_row[0] = -2;
    $sth = mysql_query("SELECT DISTINCT g.uid,g.geneId,g.chr,g.l_pos,g.r_pos,a.user_annotated_geneId from gbk_gene_annotation as g,gbk_gaeval as a where (g.uid = a.uid) && (a.props RLIKE '[[:<:]]2[[:>:]]') ORDER BY g.geneId");

    if($HTTP_POST_VARS["ShowALL"]){
      while( $row = mysql_fetch_row($sth)){
        if(($row[0] - $PREV_row[0]) == 1){
          if(($PREV_row[5])&&($row[5])){
            echo "<OPTION VALUE='$PREV_row[0]:$PREV_row[1]:$PREV_row[2]:$PREV_row[3]:$PREV_row[4]&$row[0]:$row[1]:$row[2]:$row[3]:$row[4]' style=\"color:#0000FF\">$PREV_row[1] -- $row[1]</OPTION>\n";
          }else{
            echo "<OPTION VALUE='$PREV_row[0]:$PREV_row[1]:$PREV_row[2]:$PREV_row[3]:$PREV_row[4]&$row[0]:$row[1]:$row[2]:$row[3]:$row[4]'>$PREV_row[1] -- $row[1]</OPTION>\n";
          }
        }
        $PREV_row = $row;
      }
    }else{
      $num_results = mysql_num_rows($sth);
      $magic_num = 0; $row_num = 0; $returned_results = 1;
  
      while( $row = mysql_fetch_row($sth)){
        if($row_num == $magic_num){
          // set the next magic_num
          $returned_results++;
          if($returned_results < 20){
            $magic_num = rand($magic_num + 1,( $num_results/20 * $returned_results ));
          }elseif($returned_results > 20){
            $magic_num = -1;
          }else{
            $magic_num = rand($magic_num + 1,$num_results);
          }

          // print the magic row
          if(($row[0] - $PREV_row[0]) == 1){
            if(($PREV_row[5])&&($row[5])){
              echo "<OPTION VALUE='$PREV_row[0]:$PREV_row[1]:$PREV_row[2]:$PREV_row[3]:$PREV_row[4]&$row[0]:$row[1]:$row[2]:$row[3]:$row[4]' style=\"color:#0000FF\">$PREV_row[1] -- $row[1]</OPTION>\n";
            }else{
              echo "<OPTION VALUE='$PREV_row[0]:$PREV_row[1]:$PREV_row[2]:$PREV_row[3]:$PREV_row[4]&$row[0]:$row[1]:$row[2]:$row[3]:$row[4]'>$PREV_row[1] -- $row[1]</OPTION>\n";
            }
          }else{
            $returned_results--;
            $magic_num = $row_num + 1;
          }
        }
        $row_num++;
        $PREV_row = $row;
      }
    }
    echo "</SELECT>\n";
    echo "</NOBR><BR>\n";

    echo "<P><FONT COLOR='blue'>";
    if($HTTP_POST_VARS["ShowALL"]){
      echo "<INPUT TYPE='radio' NAME=ShowALL Value=1 CHECKED ONCHANGE='document.gsFORM.submit();'> Show All Entries\n"; 
      echo "<INPUT TYPE='radio' NAME=ShowALL Value=0 ONCHANGE='document.gsFORM.submit();'> Show 20 Random Entries/List\n";
    }else{
      echo "<INPUT TYPE='radio' NAME=ShowALL Value=1 ONCHANGE='document.gsFORM.submit();'> Show All Entries\n"; 
      echo "<INPUT TYPE='radio' NAME=ShowALL Value=0 CHECKED ONCHANGE='document.gsFORM.submit();'> Show 20 Random Entries/List\n";
    }
    echo "</FONT></P>\n";    

    mysql_close($dbh);
  }
?>
<SCRIPT LANGUAGE="JavaScript">
function randomSubmit(){
  list = Math.floor(Math.random() * 5);
  if(list == 0){
    if(! document.gsFORM.NovelSeq.length){
      randomSubmit();
      return 1;
    }
    index = Math.floor(Math.random() * document.gsFORM.NovelSeq.length);
    document.gsFORM.NovelSeq.selectedIndex = index;
  }else if(list == 1){
    if(! document.gsFORM.ShortSeq.length){
      randomSubmit();
      return 1;
    }
    index = Math.floor(Math.random() * document.gsFORM.ShortSeq.length);
    document.gsFORM.ShortSeq.selectedIndex = index;
  }else if(list == 2){
    if(! document.gsFORM.SplitSeq.length){
      randomSubmit();
      return 1;
    }
    index = Math.floor(Math.random() * document.gsFORM.SplitSeq.length);
    document.gsFORM.SplitSeq.selectedIndex = index;
  }else if(list == 3){
    if(! document.gsFORM.ExtSeq.length){
      randomSubmit();
      return 1;
    }
    index = Math.floor(Math.random() * document.gsFORM.ExtSeq.length);
    document.gsFORM.ExtSeq.selectedIndex = index;
  }else if(list >= 4){
    if(! document.gsFORM.MergeSeq.length){
      randomSubmit();
      return 1;
    }
    index = Math.floor(Math.random() * document.gsFORM.MergeSeq.length);
    document.gsFORM.MergeSeq.selectedIndex = index;
  }
  
  document.gsFORM.submit();
  return 1;
}

function setGSQserver(){

  // define which web service to use
  document.gsFORM.action = "<?php echo "$GSQwebservice"; ?>";

  // open the interpretation page
  window.open("interpreting_results.htm");
  document.gsFORM.submit();
  return 1;
}
</SCRIPT>

</CENTER>

<P><FONT SIZE="+2" COLOR="#009900">STEP&nbsp;2:&nbsp; Enter your
DNA&nbsp;sequence.</FONT></P>

<BLOCKQUOTE>Now that we have a DNA&nbsp;sequence that we are
   interested in we need to enter it into the GeneSeqer program.
   There are a number of ways to enter a DNA&nbsp;sequence. You may
   enter each nitrogen base by hand, or even upload a file containing
   the sequence in it. However, the easiest way to enter your
   DNA&nbsp;sequence is by entering the GenBank accession number. To
   do this simply choose the <FONT COLOR="#FF0000">GenBank</FONT>
   format button and type the <FONT COLOR="#FF0000">accession
   number</FONT> in the appropriate box. Be sure to enter it exactly
   as it appears, small mistakes will result in failure of the search
   or searching with the wrong DNA&nbsp;sequence.
   
   <P>&nbsp;<I>Paste your genomic DNA sequence here:</I></P>
   
   <P><TEXTAREA NAME="_gdnap" ROWS=5 COLS=82 WRAP=virtual></TEXTAREA></P>
   
   <FONT COLOR="#FF0000"><I>... or type in the GenBank accession
   number of your sequence:</I><BR>
   <INPUT TYPE=text NAME=acc VALUE="<?php echo "$gbACC"; ?>" SIZE=50></FONT><BR>
   <A HREF="http://bioinformatics.iastate.edu/bioinformatics2go/gs/help.html#FORMAT" TARGET="_blank">Select
   format</A>: <INPUT TYPE=radio NAME="_l" VALUE="plain ">plain
   <INPUT TYPE=radio NAME="_l" VALUE="FASTA ">FASTA
   <FONT COLOR="#FF0000"><INPUT TYPE=radio NAME="_l" VALUE=GenBank CHECKED>GenBank</FONT><BR>
   <A HREF="http://bioinformatics.iastate.edu/bioinformatics2go/gs/help.html#SNAME" TARGET="_blank">Sequence
   name</A>: <INPUT TYPE=text NAME="_f" VALUE="" SIZE=30> (optional,
   used in <A HREF="http://bioinformatics.iastate.edu/bioinformatics2go/gs/help.html#PLAIN" TARGET="_blank">plain
   sequence format</A> only)<BR>
   <A HREF="http://bioinformatics.iastate.edu/bioinformatics2go/gs/help.html#FROMTO" TARGET="_blank">From
   position</A>: <INPUT TYPE=text NAME="_a" VALUE="<?php echo "$lpos"; ?>" SIZE=10>
   <A HREF="http://bioinformatics.iastate.edu/bioinformatics2go/gs/help.html#FROMTO" TARGET="_blank">to
   position</A>: <INPUT TYPE=text NAME="_b" VALUE="<?php echo "$rpos"; ?>" SIZE=10>
   <A HREF="http://bioinformatics.iastate.edu/bioinformatics2go/gs/help.html#STRAND" TARGET="_blank">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>
   
   The above 'position' indicator allows you to tell the program to
   only look for matches to certain segments of your
   DNA&nbsp;fragment. For instance, you may want to look for matches
   of the segment starting with base pair 510 and ending with base
   pair 12425. This is also a way to shorten a lengthy
   DNA&nbsp;fragment. To search the entire sequence just leave this
   area blank. </P>
   
   <P>You may also choose to only search in one direction along your
   sequence for potential matches. The program will automatically
   look in both directions of DNA unless you specify otherwise.
   Therefore, unless you would like this changed, simply leave the
   'both' button selected for you search.</P></BLOCKQUOTE>

<P>&nbsp;<FONT SIZE="+2" COLOR="#00CC00">STEP 3:&nbsp;Selecting
cDNA/EST sequences.</FONT></P>

<BLOCKQUOTE>This step allows you to choose which types of previously
   sequenced DNA (cDNAs &amp;&nbsp;ESTs) you would like to compare to
   your sequence. For an initial search we are going to
   <FONT COLOR="#FF0000">select the TUG button</FONT> in the
   '<FONT COLOR="#FF0000">All Plants</FONT>' category. This sequence
   collection represents the Tentative Unique Gene (TUG) clusters
   assembled using the <A HREF="http://www.plantgdb.org/ESTCluster/progress.html" TARGET="_blank">PlantGDB
   contiging method</A>. Generally, when characterizing a large
   genomic sequence, the detection of genic regions is the primary
   goal. Only after their detection, are these regions looked at in
   greater detail.
   
   <P>Spliced Alignment: The output of this selection will show an
   optimal threading of a significantly matching cDNA/EST sequence to
   your DNA by aligning putative exons (thick bars) only and
   displaying putative introns (thin bars) as (long) gaps in the
   cDNA/EST.</P>
   
<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/" TARGET="_blank">All Plants</a></td>
                 <td><input type='checkbox' name='_d' value='AllPLANTest' <?php echo "$allEST"; ?>></td>
                 <td><input type='checkbox' name='_d' value='AllPLANTtug' <?php echo "$allTUG"; ?>></td>
                 <td><input type='checkbox' name='_d' value='AllPLANTcdna' <?php echo "$allCDNA"; ?>></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/" TARGET="_blank">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/" TARGET="_blank">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/" TARGET="_blank">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'><a href="#" onClick="toggleElement(hider_list); return false;"><b>Click here to access the individual database for each species</b></a></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>
     <tr align="LEFT" id='databases'>
                 <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>

     </table>

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

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

//-->
</script>

   </P></BLOCKQUOTE>

<P><FONT SIZE="+2" COLOR="#00CC00">STEP&nbsp;4: Selecting a splice
site model</FONT></P>

<BLOCKQUOTE>This step is simply to pick the species that is most
   closely related to the DNA sequence you are interested in.</BLOCKQUOTE>

<P>

<HR>

</P>

<H2><CENTER>STEP 4:&nbsp;&nbsp;&nbsp;&nbsp;Select splice site
model</CENTER></H2>

<BLOCKQUOTE><BLOCKQUOTE><BLOCKQUOTE><BLOCKQUOTE><CENTER><A HREF="http://bioinformatics.iastate.edu/bioinformatics2go/gs/help.html#SPECIES" TARGET="_blank">Species</A>
            (selects species-specific splice site model)
            <SELECT NAME="_s">
               <OPTION VALUE=Arabidopsis SELECTED>Arabidopsis
               <OPTION VALUE=maize>maize
               <OPTION VALUE=generic>generic
            </SELECT>
            
            <HR>
            
            </CENTER></BLOCKQUOTE></BLOCKQUOTE></BLOCKQUOTE></BLOCKQUOTE>

<P><FONT SIZE="+2" COLOR="#00CC00">STEP&nbsp;5: Submitting your DNA
sequence for comparison.</FONT> </P>

<BLOCKQUOTE>Once all of the steps have been completed you are now
   ready to submit your sequence to GeneSeqer for comparison with the
   database. If you have an unusually large sequence you may want to
   have the output sent to an e-mail address, otherwise it will be
   sent to your browser. Your browser will automatically refresh
   until all of the output is on your screen.</BLOCKQUOTE>

<P>&nbsp;</P>

<H2><CENTER>STEP 5:&nbsp;&nbsp;&nbsp;&nbsp;Submit job</CENTER></H2>

<BLOCKQUOTE><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 VALUE="" SIZE=25><BR>
   <INPUT TYPE=checkbox NAME=HTML VALUE=on>HTML formatted output
   &#91;default: simple text&#93;.This option will not work if your
   mailer wraps long lines.
   
   <P>

   <INPUT TYPE=BUTTON NAME=Button VALUE="Submit" ONCLICK="setGSQserver();"> <FONT COLOR='#FF0000'><BLINK>&lt;&lt;-- Don't forget to send it to GeneSeqer!!</BLINK></FONT>
   <INPUT TYPE='hidden' NAME=RunGSQ VALUE='Submit'>
   </FORM>
   
   <HR>
   
   </P></BLOCKQUOTE>

<P><FONT SIZE="+2" COLOR="#00CC00">STEP&nbsp;6: Interpreting
Results</FONT></P>

<BLOCKQUOTE>When you receive your output from GeneSeqer you will then
   have the job of interpreting what it all means. You are encouraged
   to browse around your results and see what you can make of them.
   If you need some guidance in deciphering all of that information
   please go to the <A HREF="interpreting_results.htm" TARGET="_blank">interpreting
   results</A> page which will assist you.</BLOCKQUOTE>

</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

  GeneSeqerTutorial_files/
    AtGDB_logo.png
    BGlogo.jpg
    GSQdisplay.png
    PSI.gif
    PlantGDB.gif
    SBdetailedGSQ.png
    SBprotGSQ.png
    Thumbs.db
    image001.gif
    isu.gif
    nsflogo.gif
    pgdb.gif
    validate.js
  Exon_Intron.2.jpg
  Exon_Intron.JPG
  GeneSeqerTutorial.htm
  NCBI.logo.gif
  SBdetailedGSQ.png
  SBprotGSQ.png
  VolkerGroup.logo.jpg
  ZmDB.Logo.jpg
  fenter.jpg
  home.jpg
  index.php
  interpreting_results.htm
  pgdb.plants.gif
  sleuth.gif
  sleuth1.JPG
  terms_and_concepts.htm
  transcription.gif
  transcription1.gif
  walkthrough.php