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<div style="border-top:0px solid black;border-bottom:1px solid black;">
<font color="#D64242" size="3"><b>BLAST search.</b></font>
</div>
<br>
This page allows you to blast a nucleotide or protein sequence
against all cDNA clones, Ciona or Halocynthia EST/cDNA clones, or the
Ciona gene models.
<br>
<center>
<!--<form name="formulaire" action="blast-result.php" method="post" target="_blank">-->
<form name="formulaire" action="blast-result-TMP.php" method="post" target="_blank">

        <table width="99%" border="0" cellspacing="0" cellpadding="0">
          <tr> 
            <td align="left"><br> <br> <font color="#456898" size="2"><b>Blast type&nbsp;</b></font></td>
            <td align="left"> <br> <br> <select name="type" size="1">
                <option value="blastn">Blastn (nucleotide Vs nucleotide)</option>
                <option value="tblastx">tBlastx (nucleotide Vs translated nucleotide)</option>
                <option value="tblastn">tBlastn (protein Vs translated nucleotide)</option>
              </select> </td>
            <td align="left"><br> <br> <font color="#456898" size="2"><b>Database</b></font></td>
            <td> <br> <br> <select name="db">
		<option value="JGIwhole">Ciona intestinalis JGI v1.0 whole genome assembly</option>
		<option value="">--------------- cDNA clones ---------------</option>
                <option value="ALLclones">All cDNA clones</option>
<!-- 		<option value="XABT">Ciona intestinalis Gateway compatible clones</option> -->
                <option value="CIclones">Ciona intestinalis cDNA clones</option>
                <option value="HRclones">Halocynthia roretzi cDNA clones</option>
		<option value="">--------------- gene models ----------------</option>
                <option value="CIpredictedmRNA">Ciona intestinalis JGI gene models</option>
		<option value="KYOTOmRNA">Ciona intestinalis KyotoGrail2005 gene models</option>
		<option value="ENSmRNA">Ciona intestinalis ENSEMBL gene models</option>
		
              </select> </td>
          </tr>
	<tr>
	<td>&nbsp;</td>
	<td>&nbsp;</td>
	<td>&nbsp;</td>
	<td>&nbsp;</td>
	</tr>
          <tr> 
            <td align="left"><font color="#456898" size="2"><b>Expect: </b></font></td>
            <td align="left"> <input name="expect" type="text" value="1e-5" size="10"> 
            </td>
            <td>&nbsp;</td>
            <td>&nbsp;</td>
          </tr>
          <tr> 
            <td>&nbsp;</td>
            <td> <br> <font color="#456898" size="2"><b>Sequence in FASTA format</b></font> <br> <textarea name="sequence" rows=8 cols=40></textarea> 
            </td>
            <td align="right">&nbsp;</td>
            <td align="right">&nbsp;</td>
          </tr>
          <tr> 
            <td align="right">&nbsp;</td>
            <td align="left"> <img src="pictures/button-reset.jpg" onClick="document.formulaire.sequence.value='';document.formulaire.sequence.focus();"></td>
            <td align="right">&nbsp;</td>
            <td align="right">&nbsp;</td>
          </tr>
          <tr>
            <td align="right">&nbsp;</td>
            <td align="left">&nbsp;</td>
            <td align="right">&nbsp;</td>
            <td align="right">&nbsp;</td>
          </tr>
     <!--     <tr> 
            <td align="right"><hr color="#505F70" size="1"></td>
            <td align="left"><hr color="#505F70" size="1"></td>
            <td align="right"><hr color="#505F70" size="1"></td>
            <td align="right"><hr color="#505F70" size="1"></td>
          </tr>-->
          <tr> 
            <td align="left"><br> <font color="#456898" size="2"><b>Word Size: </b></font></td>
            <td align="left"> <br> <input name="word" type="text" value="7" size="10"> 
              &nbsp;&nbsp;&nbsp;&nbsp; <font color="#456898" size="2"><b>Matrix:</b></font> <select name = "matrix">
                <option value = "PAM30"> PAM30 </option>
                <option value = "PAM70"> PAM70 </option>
                <option value = "BLOSUM80"> BLOSUM80 </option>
                <option selected value = "BLOSUM62"> BLOSUM62 </option>
                <option value = "BLOSUM45"> BLOSUM45 </option>
              </select> </td>
            <td align="right">&nbsp;</td>
            <td align="right">&nbsp;</td>
          </tr>
          <tr> 
            <td>&nbsp;</td>
            <td> <br> <input name="filter" type="checkbox" value="T" checked> 
              <font color="#456898" size="2"><b>Filter low complexity</b></font>&nbsp;</td>
            <td align="right">&nbsp;</td>
            <td align="right">&nbsp;</td>
          </tr>
          <tr> 
            <td>&nbsp;</td>
            <td> <input name="gap" type="checkbox" value="T" checked> <font color="#456898" size="2"><b>Perform 
              a gapped alignment </b></font>&nbsp;</td>
            <td align="right">&nbsp;</td>
            <td align="right">&nbsp;</td>
          </tr>
          <tr> 
            <td>&nbsp;</td>
            <td>&nbsp;</td>
            <td align="right">&nbsp;</td>
            <td align="right"><input type="image" src="pictures/button-submit.jpg" onClick="self.submit"> 
              &nbsp;&nbsp;&nbsp;<br> &nbsp;</td>
          </tr>
        </table>
</form>
</center>





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