mason/secretom/secretary.mas

   1 <& /page/page_title.mas, title => '<span class="secretary">SecreTary</span>: Computational prediction of secreted proteins' &>
   2
   3 <& /secretom/secretary/nav.mas, curr_page => 'tool' &>
   4
   5 <&| /page/info_section.mas, title => 'Submit Sequences' &>
   6   <form id="secretary_input" method="post" action="/secretom/secretary/run" name="secretary" enctype="multipart/form-data">
   7     <div class="examples">
   8       <input type="submit" onclick="set_secretary_example_inputs(); return false;" value="Show Input Example" />
   9       <input class="reset" type="reset" name="reset" value="Clear form" />
  10     </div>
  11
  12     <label for="sequence_input_text">Paste one or more protein sequences in FASTA format</label>
  13     <textarea id="sequence_input_text" name="sequence" rows="10" cols="100"></textarea>
  14
  15     <table><tr>
  16       <td>
  17        <label for="sequence_input_file">And/or upload a FASTA file of protein sequences</label><br />
  18        <input style="margin: 0.8em 1em"   id="sequence_input_file" type="file" name="sequence_file" />
  19       </td>
  20
  21       <td>
  22        <input type="checkbox" value="Sort by score" name="sort" id="sort_by_score">
  23          <label for="sort_by_score">Sort by score</label>
  24        <br />
  25        <input type="checkbox" value="show_only_sp" name="show_only_sp" id="show_only_sp">
  26          <label for="show_only_sp">Show predicted signal peptides only</label>
  27       </td>
  28
  29       <td>
  30        <input class="submit" type="submit" name="submit" onclick="return validate_form()" value="Submit" />
  31       </td>
  32
  33     </tr></table>
  34   </form>
  35 </&>
  36
  37 <&| /page/info_section.mas, title => 'Other tools' &>
  38   <ul>
  39   <li><a href="http://www.cbs.dtu.dk/services/SignalP">SignalP</a></li>
  40   <li><a href="http://www.predisi.de">PrediSi</a></li>
  41   <li><a href="http://rpsp.bioinfo.pl/">Rapid Prediction of Signal Peptides (RPSP)</a></li>
  42   <li><a href="http://phobius.sbc.su.se/">Phobius</a></li>
  43   <li><a href="http://urgi.versailles.inra.fr/predotar/predotar.html">Predotar</a></li>
  44   </ul>
  45 </&>
  46
  47 <script language="javascript">
  48
  49 var seq_input = document.getElementById('sequence_input_text');
  50 var seq_file_input = document.getElementById('sequence_input_file');
  51 function set_secretary_example_inputs() {
  52         seq_input.value = ">AT1G73440.1  \nMARGESEGESSGSERESSSSSSGNESEPTKGTISKYEKQRLSRIAENKARLDALGISKAAKALLSPSPVSKKRRVKRNSGEEDDDYTPVIADGDGDEDDDEVEEIDEDEEFLCKRKNKSSASKRKVSSRKILNTSVSLGEDDDDLDKAIALSLQGSVAGSDKEAATMKKKRPELMSKTQMTQDELVMYFCQFDEGGKGFITLRDVAKMATVHDFTWTEEELQDMIRCFDMDKDGKLSLDEFRKIVSRCRMLKGS* \n>AT1G75120.1 AI22=119.545 Gravy22=0.5864 nR=2 nS=0 nT=0 nDRQPEN=6 Nitrogen=31 Oxygen=27 \nMAVRKEKVQPFRECGIAIAVLVGIFIGCVCTILIPNDFVNFRSSKVASASCESPERVKMFKAEFAIISEKNGELRKQVSDLTEKVRLAEQKEVIKAGPFGTVTGLQTNPTVAPDESANPRLAKLLEKVAVNKEIIVVLANNNVKPMLEVQIASVKRVGIQNYLVVPLDDSLESFCKSNEVAYYKRDPDNAIDVVGKSRRSSDVSGLKFRVLREFLQLGYGVLLSDVDIVFLQNPFGHLYRDSDVESMSDGHDNNTAYGFNDVFDDPTMTRSRTVYTNRIWVFNSGFFYLRPTLPSIELLDRVTDTLSKSGGWDQAVFNQHLFYPSHPGYTGLYASKRVMDVYEFMNSRVLFKTVRKDEEMKKLKPVIIHMNYHSDKLERMQAAVEFYVNGKQDALDRFRDGS* \n>AT1G17600.1 AI22=61.818 Gravy22=-0.2273 nR=2 nS=5 nT=0 nDRQPEN=6 Nitrogen=29 Oxygen=34 \nMVSSSAPRVSKYDVFLSFRGEDTRKTIVSHLYAALDSRGIVTFKDDQRLEIGDHISDELHRALGSSSFAVVVLSENYATSRWCLLELQLIMELMKEGRLEVFPIFYGVDPSVVRHQLGSFSLVKYQGLEMVDKVLRWREALNLIANLSGVVSSHCVDEAIMVGEIARDISRRVTLMHKIDSGNIVGMKAHMEGLNHLLDQESNEVLLVGIWGMGGIGKTSIVKCLYDQLSPKFPAHCFIENIKSVSKDNGHDLKHLQKELLSSILCDDIRLWSVEAGCQEIKKRLGNQKVFLVLDGVDKVAQVHALAKEKNWFGPGSRIIITTRDMGLLNTCGVEVVYEVKCLDDKDALQMFKQIAFEGGLPPCEGFDQLSIRASKLAHGLPSAIQAYALFLRGRTASPEEWEEALGALESSLDENIMEILKISYEGLPKPHQNVFLHVVCLFNGDTLQRITSLLHGPIPQSSLWIRVLAEKSLIKISTNGSVIMHKLVEQMGREIIRDDMSLARKFLRDPMEIRVALAFRDGGEQTECMCLHTCDMTCVLSMEASVVGRMHNLKFLKVYKHVDYRESNLQLIPDQPFLPRSLRLFHWDAFPLRALPSGSDPCFLVELNLRHSDLETLWSGTPSNGVKTENPCEKHNSNYFHVLLYLAQMLKSLKRLDVTGSKHLKQLPDLSSITSLEELLLEQCTRLEGIPECIGKRSTLKKLKLSYRGGRRSALRFFLRKSTRQQHIGLEFPDAKVKMDALINISIGGDITFEFRSKFRGYAEYVSFNSEQQIPIISAMSLQQAPWVISECNRFNSLRIMRFSHKENGESFSFDVFPDFPDLKELKLVNLNIRKIPSGICHLDLLEKLDLSGNDFENLPEAMSSLSRLKTLWLQNCFKLQELPKLTQVQTLTLTNCRNLRSLAKLSNTSQDEGRYCLLELCLENCKSVESLSDQLSHFTKLTCLDLSNHDFETLPSSIRDLTSLVTLCLNNCKKLKSVEKLPLSLQFLDAHGCDSLEAGSAEHFEDIPNKEVNTWLLIRLYYD* \n";
  53 }
  54
  55 function validate_form() {
  56   if( seq_input.value || seq_file_input.value )
  57         return true;
  58
  59   alert('No sequence entered, please paste or upload sequence data to run SecreTary.');
  60   return false;
  61 }
  62
  63 </script>