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    <td nowrap> 
    <h2><font face="Arial, Helvetica, sans-serif" color="#003366">YASPIN
secondary structure prediction</font></h2>
 </td>
  </tr>
</table>
<blockquote>
<table height="90%"BORDER=0 CELLPADDING=0 CELLSPACING=0 align=left>
<tr VALIGN=TOP>
<td width=150 valign=top>
<br><img border=1 SRC="helices.gif">
<font face="Arial, Helvetica, sans-serif" size="2">
<br><br>
<a href="help.php"><b>Options Help</b></a>
<br><br>
<b>YASPIN</b> is a HNN (Hidden Neural Network) secondary structure
prediction program that uses the PSI-BLAST algorithm to produce a PSSM
for the input sequence, which it then uses to perform its prediction.
<br>
<br>
<b>Reference:</b> Lin K., Simossis V.A., Taylor W.R. and Heringa J.
(2005) A Simple and Fast Secondary Structure Prediction Algorithm using
Hidden Neural Networks. Bioinformatics. 21(2):152-9. (Epub 2004 Sep 17).
<a target=_new
href="
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15377504
"><b>Abstract</b></a>
</font>
</td>
<td valign=top width=30>&nbsp;</td>
</tr>
</table>
<table BORDER=0 CELLPADDING=0 CELLSPACING=0>
<form METHOD="POST" enctype='multipart/form-data'>
<tr VALIGN=TOP> 
<td colspan="2">
<font face="Arial, Helvetica, sans-serif" size="2"><b>Paste in your
protein sequence in FASTA format:</b><a href="help.php">Help</a><br>
<textarea NAME="seq" MAXLENGTH="80" ROWS="10"
COLS="80"></textarea></font>
</td>
</tr>
<tr>
<td>
<font face="Arial, Helvetica, sans-serif" size="2"><br>
<b>Or Upload a FASTA file: </b><a href="help.php">Help</a>
<br><input TYPE="file" NAME='seq_file' SIZE=30>
</font>
</td>
<td align=left>
<font face="Arial, Helvetica, sans-serif" size="2"><br>
&nbsp;&nbsp;&nbsp;<b>Upload a PSSM for your sequence (if applicable):
</b><a href="help.php">Help</a><br>
&nbsp;&nbsp;&nbsp;<input TYPE="file" NAME='pssm_file'
SIZE=30></font><br>
</td>
</tr>
<tr>
<td colspan="2">
<font face="Arial, Helvetica, sans-serif" size="2"><br>
<b>Enter a name for your job: </b><a href="help.php">Help</a><br>
<input type="text" name="mbjob[description]" value="YASPIN Job">
</font>
</td>
</tr>
<tr>
<td>
<font face="Arial, Helvetica, sans-serif" size="2"><br>
<b>Choose a database for PSI-BLAST to use: </b> <a
href="help.php">Help</a><br>
<SELECT NAME="smethod" SIZE ="1">
<OPTION value="nr" SELECTED>NR</OPTION>
<OPTION value="swissprot">SWISSPROT</OPTION>
<OPTION value="pdbaa">PDB</OPTION>
<OPTION value="scop10">SCOP10</OPTION>
<OPTION value="scop20">SCOP20</OPTION>
<OPTION value="scop25">SCOP25</OPTION>
<OPTION value="scop30">SCOP30</OPTION>
<OPTION value="scop35">SCOP35</OPTION>
<OPTION value="scop40">SCOP40</OPTION>
<OPTION value="scop50">SCOP50</OPTION>
<OPTION value="scop70">SCOP70</OPTION>
</SELECT>
</font>
</td>
<td align=left>
<font face="Arial, Helvetica, sans-serif" size="2"><br>
&nbsp;&nbsp;&nbsp;<b>Choose the NN you would like to use: </b> <a
href="help.php">Help</a><br>
&nbsp;&nbsp;&nbsp;<SELECT NAME="nnmethod" SIZE ="1">
<OPTION value="dssp" SELECTED>DSSP-trained</OPTION>
<OPTION value="stride">STRIDE-trained</OPTION>
</SELECT>
</font>
</td>
</tr>
<tr>
<td colspan="2">
<font face="Arial, Helvetica, sans-serif" size="2"><br>
<b>(NB: server results have a maximum lifetime of 15 days): </b><a
href="help.php">Help</a><br>
<b>Also send me the results by email &nbsp;&nbsp;<input type="checkbox"
name="emailsw" value ="on" CHECKED><br><br>
<b>My email address is <input type="text" size="30" name="email"> 
<br><br>
<!-- Do you want to choose your own colours for viewing the prediction?
<a href="help.php#colour schemes">Help</a>
<INPUT TYPE="radio" NAME="usercs" VALUE="yes"> YES  
<INPUT TYPE="radio" NAME="usercs" VALUE="no" CHECKED> NO
<br><br> -->
<INPUT TYPE="submit" NAME="yaspin_align" VALUE="YASPIN prediction">
<input type="reset" VALUE="Clear Input">
<input type="hidden" name="mbjob[method]" value="yaspin">
</font>
</td>
</tr>
</form>
</table>
<br><br><table>
<tr>
<td bgcolor="#003366" align="center"><font face="Arial, Helvetica,
sans-serif" size="2"><font color="#FFFFFF" size=-1>Interface written by
</font><a href="mailto:
vsi...@cs.vu.nl
"><font color="#FFFFCC"
size=-1>Victor A. Simossis</font></a><font color="#FFFFFF" size=-1> and
</font><a href="mailto:
kx...@nimr.mrc.ac.uk
"><font color="#FFFFCC"
size=-1>Kuang Lin</font></a>
</font></td>
</tr>
</table><br>
<font style="font-family: Arial,Helvetica,sans-serif; font-size: 11px">
(c) IBIVU 2006. If you are experiencing problems with the
site, please contact the <a href="mailto:
ib...@cs.vu.nl
">webmaster</a>.
</font>
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Si ma perchè non risponde poi con i risultati quando io gli mando le
coppie
(nome input,valore)?
Uso il seguente codice
URL YaspinUrl = new URL("
http://ibivu.cs.vu.nl/programs/yaspinwww/
");
//URL a cui si ci deve connettere
            try {
                URLConnection connection = YaspinUrl.openConnection();
//si connette all'URL
                connection.setDoOutput(true); //imposta la connessione
per l'output
                PrintWriter out = new
PrintWriter(connection.getOutputStream());
                out.print("seq" + "=" +
URLEncoder.encode(primaryStrSequence) + "&");
                out.print("mbjob[description]" + "=" +
URLEncoder.encode("YASPIN Job") + "&");
                out.print("smethod" + "=" + URLEncoder.encode("nr") +
"&");
                out.print("nnmethod" + "=" + URLEncoder.encode("dssp") +
"&");
                out.print("emailsw" + "=" + URLEncoder.encode("on") +
"&");
                out.print("email" + "=" +
URLEncoder.encode("
secondary...@jumpy.it
"));
                out.print("mbjob[method]" + "=" +
URLEncoder.encode("yaspin"));
                out.close(); 


 Uso il seguente codice
A occhio direi che:
a) Manca sicuramente il Content Type
b) Perché non usi HttpURLConnection?
c) Manca il POST, e può darsi che usando il PrintWriter su URLConnection non
ti venga automaticamente impostato (nel caso prova DataOutputStream, se non
vuoi passare a HttpURLConnection)
Ma non sono uno sviluppatore java, spippolo a tempo perso su J2ME, quindi ti
conviene chiedere nel NG che ti ho indicato.
-- 
~ Tenete la morte lontano dalle strade. Guidate sul marciapiede.