Motif & Logo Analysis Tools

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if (!page.match(item + ".jsp")) { document.getElementById(item).src = source; } } function checkErrors() { return true; } </script> <link rel="stylesheet" type="text/css" href="/dist/6.7.7_1/css/jquery-ui.css"> <script src="https://www.google.com/jsapi?key=ABQIAAAAtZh6pEZC7czy0aX8i1CHRhTIAbWi2SkPYTYrkqszX-mDTQdcXBQEmWIZrgiXodyNuAxSrxLNLnMxIw" type="text/javascript"></script> <script type="text/javascript"> /* <![CDATA[ */ $(document).ready(function(){ //Set the initial values for the form if ($("input[name='motifSearchAlgorithm']:checked").length == 0) { $("input[name='motifSearchAlgorithm'][value='MotifAll']").attr('checked', 'checked'); } if($("input[name='motifSearchAlgorithm']:checked").val() == 'MotifAll') { hideDivById('minMatchesDiv'); showDivById('supportThresholdDiv'); } else { hideDivById('supportThresholdDiv'); showDivById('minMatchesDiv'); } if ($("input[name='motifSearchBackground']:checked").length == 0) { $("input[name='motifSearchBackground'][value='AUTO']").attr('checked', 'checked'); } if ($("input[name='background']:checked").length == 0) { $("input[name='background'][value='Y']").attr('checked', 'checked'); } if ($("input[name='algorithm']:checked").length == 0) { $("input[name='algorithm'][value='freqTimesLogFold']").attr('checked', 'checked'); } if($("#motifSearchThreshold").val() == '') { $("#motifSearchThreshold").val("1e-06"); } if($("#motifSearchMinimumMatches").val() == '') { $("#motifSearchMinimumMatches").val("10"); } if($("#motifSearchSupportThreshold").val() == '') { $("#motifSearchSupportThreshold").val("0.05"); } }); /* ]]> */ </script> <style type="text/css"> body { font-size:100%; } p { margin:0; padding:0; } .toolTip {color:#036; font-weight:normal; text-decoration:underline;} .foreground-ds { float:left; width:400px; } .generator-settings { width:515px; float:right; padding-bottom:20px;} .submitButton { clear:both; margin:0 0 0 430px;} </style> <div class="dataContainer"> <div style="width:980px; margin-top:1em; margin-left:1em"> <div id="motifAnalysisId"> <form id="sequenceLogoSubmitAction" name="SequenceLogoForm" action="/sequenceLogoSubmitAction.action;jsessionid=FCDA887B05BBA33C3E2AAC9ED9576493" method="POST" enctype="multipart/form-data"> <input type="hidden" name="what" value="motif" id="sequenceLogoSubmitAction_what"/> <div class="foreground-ds"> <p><b>Foreground data set</b>: submit prealigned sequences of 15 residues or less (15, 13, 11, etc). The modification site needs to be centrally located for correct statistical analysis.</p> <p style="padding-top:10px;"><b>Paste Sequence Data:</b></p> <textarea name="sequence" cols="50" rows="8" id="seqdata1" class="fieldBox" style="resize:vertical;"></textarea> <p style="padding-top:10px;">Upload Sequence File: <input type="file" name="sequenceFile" value="" id="sequenceLogoSubmitAction_sequenceFile"/></p> </div> <div class="generator-settings"> <table cellpadding="0" cellspacing="0" border="0" width="515"> <tr> <td style="padding-bottom:10px; color:#000; font-weight:bold;" colspan="2">Motif Analysis Generator Settings</td> </tr> <tr> <td valign="top" align="left" style="padding-bottom:20px; width:155px;">Title:</td> <td valign="top" align="left"><input type="text" name="motifSearchTitle" size="40" maxlength="80" value="" id="motifSearchTitle"/></td> </tr> <tr> <td valign="top" align="left" style="padding-bottom:20px;">Algorithm:</td> <td valign="top" style="padding-bottom:10px;" align="left"> <table cellpadding="0" cellspacing="0" border="0"> <tr> <td valign="top" align="left" style="padding-bottom:5px;padding-right:75px;"> <input type="radio" name="motifSearchAlgorithm" id="MotifAll" value="MotifAll" onclick="hideDivById('minMatchesDiv');showDivById('supportThresholdDiv');"/><label for="MotifAll"> <a href="#" class="toolTip" title="He, Z., Yang, C., Guo, G. et al. Motif-All: discovering all phosphorylation motifs. BMC Bioinformatics 12, S22 (2011). https://doi.org/10.1186/1471-2105-12-S1-S22">MotifAll</a>  </label> </td> <td valign="top" align="left" style="padding-bottom:5px;"> <input type="radio" name="motifSearchAlgorithm" id="sequenceLogoSubmitAction_motifSearchAlgorithmbinom2aa" value="binom2aa" onclick="hideDivById('supportThresholdDiv');showDivById('minMatchesDiv');"/><label for="sequenceLogoSubmitAction_motifSearchAlgorithmbinom2aa"> Exhaustive 1-2 AA  </label> </td> </tr> </table> </td> </tr> <tr> <td valign="top" align="left" style="padding-bottom:20px;"> <a href="#" class="toolTip" title="Background sequence datasets are extracted from all proteins in PhosphoSitePlus that contain the selected modification type. Sequences surrounding all residues of the selected type of amino acid within the target proteins are included regardless of their modification status.">Background based on</a>: </td> <td valign="top" style="padding-bottom:10px;" align="left"> <table cellpadding="0" cellspacing="0" border="0"> <tr> <td valign="top" align="left" style="padding-bottom:5px;"> <input type="radio" name="motifSearchBackground" id="sequenceLogoSubmitAction_motifSearchBackgroundS" value="S"/><label for="sequenceLogoSubmitAction_motifSearchBackgroundS"> ph<a href="#" class="toolTip" title="Tip for Ser">Ser</a> Proteins  </label> </td> <td valign="top" align="left" style="padding-bottom:5px;"> <input type="radio" name="motifSearchBackground" id="sequenceLogoSubmitAction_motifSearchBackgroundT" value="T"/><label for="sequenceLogoSubmitAction_motifSearchBackgroundT"> ph<a href="#" class="toolTip" title="Tip for Thr">Thr</a> Proteins  </label> </td> </tr> <tr> <td valign="top" align="left" style="padding-bottom:5px;"> <input type="radio" name="motifSearchBackground" id="sequenceLogoSubmitAction_motifSearchBackgroundY" value="Y"/><label for="sequenceLogoSubmitAction_motifSearchBackgroundY"> phTyr Proteins  </label> </td> <td valign="top" align="left" style="padding-bottom:5px;"> <input type="radio" name="motifSearchBackground" id="sequenceLogoSubmitAction_motifSearchBackgroundACETYL_K" value="ACETYL_K"/><label for="sequenceLogoSubmitAction_motifSearchBackgroundACETYL_K"> acLys Proteins  </label> </td> </tr> <tr> <td valign="top" align="left"> <input type="radio" name="motifSearchBackground" id="sequenceLogoSubmitAction_motifSearchBackgroundAUTO" value="AUTO"/><label for="sequenceLogoSubmitAction_motifSearchBackgroundAUTO"> Automatic Selection  </label> </td> <td valign="top" align="left"> <input type="radio" name="motifSearchBackground" id="sequenceLogoSubmitAction_motifSearchBackgroundUBI_K" value="UBI_K"/><label for="sequenceLogoSubmitAction_motifSearchBackgroundUBI_K"> UbLys Proteins  </label> </td> </tr> </table> </td> </tr> <tr> <td valign="top" align="left" style="padding-bottom:10px; width:155px;">Significance:</td> <td valign="top" style="padding-bottom:10px;" align="left"> <table cellpadding="0" cellspacing="0" border="0"> <tr> <td width="180" valign="top" align="left"> <input type="text" name="motifSearchThreshold" size="8" maxlength="80" value="" id="motifSearchThreshold"/> </td> </tr> <tr> <td><span class="fieldTitle">E.g. 1e-06 or 0.000001</span></td> </tr> </table> </td> </tr> <tr id="minMatchesDiv" style="display:none"> <td valign="top" align="left"> <div id="minMatches" style="padding-bottom:20px; width:155px;">Occurrences:</div> </td> <td valign="top" align="left"> <table cellpadding="0" cellspacing="0" border="0"> <tr> <td width="180" valign="top" align="left"> <div id="minMatchesText" style="padding-bottom:10px;"> <input type="text" name="motifSearchMinimumMatches" size="8" maxlength="80" value="" id="motifSearchMinimumMatches"/> </div> </td> </tr> </table> </td> </tr> <tr id="supportThresholdDiv" style="display:none"> <td valign="top" align="left"> <div id="supportThreshold" style="padding-bottom:20px; width:155px;"><a href="#" class="toolTip" title="The Support Threshold corresponds to the subset of the foreground dataset that must contain a given motif before it is reported as a hit. The default value for the minimum support is 5%.">Support Threshold</a>:</div> </td> <td valign="top" align="left"> <table cellpadding="0" cellspacing="0" border="0"> <tr> <td width="180" valign="top" align="left"> <div id="supportThresholdText" style="padding-bottom:10px;"> <input type="text" name="motifSearchSupportThreshold" size="8" maxlength="80" value="" id="motifSearchSupportThreshold"/>  </div> </td> </tr> </table> </td> </tr> <tr> <td valign="top" align="left"> <a href="#" class="toolTip" title="Sets of background sequences have to be aligned with the modified residue located at the center of the sequence. The length of the background sequences must be at least as long as the length of the foreground sequences.">Upload Background</a>: </td> <td valign="top" align="left"> <input type="file" name="motifSearchBackgroundFile" value="" id="sequenceLogoSubmitAction_motifSearchBackgroundFile"/> </td> </tr> </table> </div> <div class="submitButton"> <input type="submit" value="Generate" class="searchButton"> </div> </form> </div> </div> </div> <style type="text/css"> .footer { display: none; position: absolute; left: 0; bottom: 0; height: auto; width: 100%; } .footerContent { width: 100%; background: #3e7998 url(//media.cellsignal.com/www/images/project-images/img/assets/background-header@15.png) no-repeat scroll bottom center; } .containerFooter { width: 1000px; position:relative; margin:auto; padding: 5px 0px 5px 20px; } .containerFooter td { color: white; } .containerFooter tr { vertical-align: middle; } .containerFooter img { vertical-align: middle; } .bottomHeader { width: 1000px; margin:auto; text-align: center; font-family: Verdana, Arial, Helvetica, sans-serif; font-size: 12px; color: black; } </style>  <div class="footer"> <div class="footerContent"> <table width="100%" border="0" cellspacing="0" cellpadding="1" class="containerFooter"> <tr> <td width="25%" valign="top">Developed with grants from  <a href="https://www.nih.gov/" target="_blank"> <img src="images/footer/logo_nih.png" alt="NIH Logo" /> </a> </td> <td width="32%" valign="top">and literature mining with Linguamatics  <a href="https://www.linguamatics.com/" target="_blank"> <img src="images/footer/logo_i2e.png" alt="I2E Logo" /> </a> </td> <td> <a href="https://creativecommons.org/licenses/by-nc-sa/3.0/"> <img src="images/footer/logo_ccLicense.png" alt="Creative Commons License" align="left" height="30px"/> </a>PhosphoSite, created by Cell Signaling Technology is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. </td> </tr> </table> </div> <div style="background-color: #666666;"> <p class="bottomHeader" style="padding: 5px 0px;color:#FFFFFF">©2003-2024 Cell Signaling Technology, Inc. </p> </div> </div> <script>(function(){function c(){var b=a.contentDocument||a.contentWindow.document;if(b){var d=b.createElement('script');d.innerHTML="window.__CF$cv$params={r:'9199865cbc27fd40',t:'MTc0MDg0MTIzNi4wMDAwMDA='};var a=document.createElement('script');a.nonce='';a.src='/cdn-cgi/challenge-platform/scripts/jsd/main.js';document.getElementsByTagName('head')[0].appendChild(a);";b.getElementsByTagName('head')[0].appendChild(d)}}if(document.body){var a=document.createElement('iframe');a.height=1;a.width=1;a.style.position='absolute';a.style.top=0;a.style.left=0;a.style.border='none';a.style.visibility='hidden';document.body.appendChild(a);if('loading'!==document.readyState)c();else if(window.addEventListener)document.addEventListener('DOMContentLoaded',c);else{var e=document.onreadystatechange||function(){};document.onreadystatechange=function(b){e(b);'loading'!==document.readyState&&(document.onreadystatechange=e,c())}}}})();</script></body> </html>

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Motif & Logo Analysis Tools