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<TD class="DocTitleText" align="left"> <A HREF="../lexington.cgi">CDART <!-- SPAN class="DocTitleTextSmall13">Conserved Domain Architecture Retrieval Tool</SPAN --></A> Help</TD>
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<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="cdart_about.html"> ABOUT </A></TD>
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<!-- TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="cdart_how_to.html"> HOW TO </A></TD -->
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<TD class="NavResourceButtonActive" align="center" valign="center" style="white-space: nowrap;"><A href="cdart_help.html"> HELP </A></TD>
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<!-- TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="cdart_tools.html"> TOOLS </A></TD -->
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<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="cdart_publications.html"> PUBLICATIONS </A></TD>
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<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="../../cdd/cdd.shtml"> RESOURCES </A></TD>
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<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="../../cdd/docs/cdd_news.html"> NEWS </A></TD>
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<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="../../structure_discover.html"> DISCOVER </A></TD>
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<TD class="WhiteCell NormalText" width="10" align="center"> </TD>
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<TD class="WhiteCellBlueEdgeAll ThumbText2" align="center">
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<SPAN class="MiniText"> <BR></SPAN>
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<P class="indent20bottomspace">This help document describes how to use <A HREF="../lexington.cgi"><B>CDART</B></A>, including detailed descriptions of the input required, output displays, and the program's features and functions. The <A HREF="../../cdd/cdd.shtml"><B>Conserved Domains resources</B></A> page describes additional, related resources and provides "<A HREF="../../cdd/docs/cdd_how_to.html"><B>How To</B></A>" guides that illustrate how those resources can be used.</P>
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<!-- P class="indent20bottomspace">Once records of interest are retrieved, follow Entrez's "Links" to <A HREF="../../structure_discover.html"><B>discover associations among previously disparate data</B></A>.</P -->
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<TD class="WhiteCell NormalText" width="10" align="center"> </TD>
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</TR>
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<!-- ==================== TOC_TABLE_OF_CONTENTS ================= -->
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<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#F0F8FF">
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<!-- TABLE width="100%" border="0" class="Yellow1CellBlueEdge ThumbText2">
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<TD ALIGN="Center" VALIGN="TOP" class="Yellow1Cell" style="white-space: nowrap;">DETAILED TABLE OF CONTENTS</TD>
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</TR>
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</TABLE -->
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<A NAME="TOCWhatIs"></A>
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<UL>
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<LI><A HREF="#WhatIs">What is <B>CDART</B>?</A></LI>
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<UL>
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<LI><!-- A HREF="#PCClusterDefinition" --><A HREF="#WhatIs"><B>C</B>onserved <B>D</B>omain <B>A</B>rchitecture <B>R</B>etrieval <B>T</B>ool</A></LI>
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<!-- LI><A HREF="#DatabaseApplications">How can CDART be used to learn more about proteins?</A></LI>
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<UL>
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<LI><A HREF="#DatabaseApplications________">________________</A></LI>
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<LI><A HREF="#DatabaseApplications________">________________</A></LI>
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<LI><A HREF="#DatabaseApplications________">________________</A></LI>
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</UL -->
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</UL>
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</UL>
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<A NAME="TOCQuickStart"></A>
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<UL>
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<LI><A HREF="#QuickStart"><B>Quick start</B> guide</A></LI>
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<UL>
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<LI><A HREF="#QuickStart">illustrated example showing the <SPAN style="color:#D70000">1-2-3 step process</SPAN> for using the tool</A></LI>
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</UL>
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</UL>
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<A NAME="TOCInput"></A>
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<UL>
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<LI><A HREF="#Input"><B>Input Options</B></A></LI>
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<UL>
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<LI><A HREF="#InputCDARThomepage"><B>enter query directly into CDART home page</B></A></LI>
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<UL>
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<LI><A HREF="#InputProtein">as a <B>protein sequence</B></A></LI>
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<UL>
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<LI><A HREF="#InputProteinUID">protein unique identifiers (UIDs)</A></LI>
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<LI><A HREF="#InputProteinSequence">protein sequence data</A></LI>
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</UL>
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<LI><A HREF="#InputConservedDomainSet">as a <B>set of conserved domains (CDs)</B></A></LI>
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<UL>
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<LI><A HREF="#InputConservedDomainSetClusterIDs">conserved domain superfamily cluster IDs</A></LI>
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<LI><A HREF="#InputConservedDomainSetPSSMIDs">PSSM IDs for specific domain models</A></LI>
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<LI><A HREF="#InputConservedDomainSetClusterIDsAndPSSMIDs">mix of superfamily cluster IDs and PSSM IDs</A></LI>
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</UL>
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<LI><A HREF="#InputMultipleQueries">enter <B>multiple queries</B></A></LI>
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</UL>
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<LI><A HREF="#InputEntrezSearch"><B>retrieve sequence record from Entrez Protein</B></A></LI>
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<UL>
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<LI><A HREF="#InputEntrezProteinDomainRelatives">follow the "Domain relatives" link</A></LI>
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</UL>
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<!-- LI><A HREF="#________"><B>________</B></A></LI>
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<UL>
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<LI><A HREF="#________">________</A></LI>
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<LI><A HREF="#________">________</A></LI>
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<LI><A HREF="#________">________</A></LI>
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<LI><A HREF="#________">________</A></LI>
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<LI><A HREF="#________">________</A></LI>
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<LI><A HREF="#________">________</A></LI>
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</UL>
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</UL -->
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</UL>
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</UL>
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<A NAME="TOCOutput"></A>
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<UL>
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<LI><A HREF="#Output"><B>Output Display</B></A></LI>
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<UL>
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<LI><A HREF="#OutputGraphicalSummary"><B>graphical summary of similar domain architectures</B></A></LI>
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<UL>
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<LI><A HREF="#OutputQuery">query</A></LI>
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<LI><A HREF="#OutputList">list of similar domain architectures</A></LI>
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</UL>
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<LI><A HREF="#OutputFilters"><B>Filter your results</B></A></LI>
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<UL>
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<LI><A HREF="#OutputFilters">refine your results to include/exclude conserved domain superfamilies</A></LI>
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</UL>
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<LI><A HREF="#OutputDomainArchitecture"><B>information provided for each domain architecture</B></A></LI>
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<UL>
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<LI><A HREF="#OutputDomainArchitectureTitle">title</A></LI>
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<LI><A HREF="#OutputDomainArchitectureTaxonomicSpan">taxonomy span</A></LI>
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<LI><A HREF="#OutputDomainArchitectureSimilarityScore">similarity score</A></LI>
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<LI><A HREF="#OutputDomainArchitectureTotalNrSequences">total nr sequences</A></LI>
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<LI><A HREF="#OutputDomainArchitectureLookupSequencesInEntrez">lookup sequences in Entrez</A></LI>
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<!--
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<LI><A HREF="#OutputDomainArchitectureExpandedView">[+]/[-] to expand/contract display for individual domain architecture</A></LI>
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<UL>
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<LI><A HREF="#OutputDomainArchitectureShowNrRepresentatives">list of representative, non-redundant protein sequences</A></LI>
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<LI><A HREF="#OutputDomainArchitectureDomainDetails">"domain details" link</A></LI>
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LI><A HREF="#OutputDomainArchitectureExpandedViewIllustration">illustrated example</A></LI>
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</UL>
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</UL>
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-->
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<A NAME="TOCDefinitions"></A>
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<!-- UL>
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<LI><A HREF="#Definitions"><B>Definitions & Algorithm Details</B></A></LI>
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<UL>
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<LI><A HREF="#________"><B>________</B></A></LI>
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<UL>
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</UL>
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</UL -->
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<A NAME="TOCReferences"></A>
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<UL>
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<LI><A HREF="#References"><B>References</B></A></LI>
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<UL>
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<LI><A HREF="#Citing">Citing CDART</A></LI>
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<!-- LI><A HREF="#ReferencesSupportedDatabases">References describing the supported databases</A></LI -->
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<!-- SECTION_HEADER:
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<A NAME="TOC__anchorname___"></A>
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<LI><A HREF="#__anchorname___"><B>_____Section_Header_____</B></A></LI>
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<LI><A HREF="#________"><B>________</B></A></LI>
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</UL -->
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<!-- ======= SPACER_COLUMN_TO_RIGHT_OF_TOC_LEFT_SIDE_TEXT ========= -->
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<TD class="WhiteCell TOCText" width="5"> </TD>
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<!-- =============== RIGHT_SIDE_THUMBNAILS ================ -->
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<TD WIDTH="370" class="WhiteCell ThumbText" ALIGN="LEFT" VALIGN="TOP">
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<!-- BR -->
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<!-- =============== BRIEF_TABLE_OF_CONTENTS ================ -->
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<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0">
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<TR>
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<TD class="WhiteCell ThumbText2" ALIGN="Left" VALIGN="TOP">
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<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" class="Yellow1CellBlueEdge ThumbText2">
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<TR>
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<TD ALIGN="Center" VALIGN="TOP" class="Yellow1Cell" style="white-space: nowrap;">BRIEF TABLE OF CONTENTS</TD>
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</TR>
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</TABLE>
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<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" class="Yellow1CellBlueEdgeBottomAndSides ThumbText2">
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<TD ALIGN="Left" class="MicroText Yellow1Cell" VALIGN="TOP" colspan="3"> </TD>
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</TR>
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<TR>
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<TD ALIGN="Left" class="MiniText Yellow1Cell" VALIGN="TOP"> </TD>
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<TD ALIGN="Left" VALIGN="TOP" style="white-space: nowrap;" class="Yellow1Cell">
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<A HREF="#WhatIs">What is CDART?</A><BR>
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<img SRC="/Structure/IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#WhatIs"><B>C</B>onserved <B>D</B>omain <B>A</B>rchitecture <B>R</B>etrieval <B>T</B>ool</A><BR>
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<!-- img SRC="/Structure/IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#DatabaseApplications">What can it show about proteins?</A><BR -->
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<BR>
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<A HREF="#QuickStart">Quick start guide</A><BR>
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<img SRC="/Structure/IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#QuickStartIllustration">1-2-3 step process <SPAN style="color:#D70000"><I>(illustration)</I></SPAN></A><BR><BR>
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<A HREF="#Input">Input options</A><BR>
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<img SRC="/Structure/IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#InputCDARThomepage">Enter query into CDART home page</A><BR>
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<img SRC="/Structure/IMG/spacer.gif" width="60" height="1" border="0"><A HREF="#InputProtein">- protein sequence</A><BR>
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<img SRC="/Structure/IMG/spacer.gif" width="60" height="1" border="0"><A HREF="#InputConservedDomainSet">- set of conserved domains (CDs)</A><BR>
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<img SRC="/Structure/IMG/spacer.gif" width="60" height="1" border="0"><A HREF="#InputMultipleQueries">- multiple queries</A><BR>
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<img SRC="/Structure/IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#InputEntrezSearch">Retrieve Entrez Protein sequence record</A><BR>
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<img SRC="/Structure/IMG/spacer.gif" width="60" height="1" border="0"><A HREF="#InputEntrezSearchDomainRelativesLink">- follow "Domain Relatives" link</A><BR>
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<!-- img SRC="/Structure/IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#______">___________</A><BR -->
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<BR>
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<A HREF="#Output">Output Display</A><BR>
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<img SRC="/Structure/IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#OutputGraphicalSummary">Graphical summary of similar architectures</A><BR>
|
|
<img SRC="/Structure/IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#OutputFilters">Filter your results</A><BR>
|
|
<img SRC="/Structure/IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#OutputDomainArchitecture">Details for individual domain architecture</A><BR>
|
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<!-- img SRC="/Structure/IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#______">___________</A><BR -->
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<BR>
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<!-- A HREF="#Definitions">Definitions & Algorithm Details</A><BR>
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<img SRC="/Structure/IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#Definitions______">____________</A><BR>
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<img SRC="/Structure/IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#Definitions______">____________</A><BR>
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<img SRC="/Structure/IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#Definitions______">____________</A><BR>
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<img SRC="/Structure/IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#______">___________</A><BR -->
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<A HREF="#References">References</A><BR>
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<!-- A HREF="#___">_________</A><BR -->
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</TD>
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<TD ALIGN="Left" class="MiniText Yellow1Cell" VALIGN="TOP"> </TD>
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</TR>
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<TR>
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<TD ALIGN="Left" class="MicroText Yellow1Cell" VALIGN="TOP" colspan="3"> </TD>
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</TR>
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</TABLE>
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<TD class="WhiteCell ThumbText2" ALIGN="Left" VALIGN="TOP" WIDTH="10"> </TD>
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</TR>
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</TABLE>
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<BR>
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<!-- ======= SINGLE_THUMBNAIL_YELLOW_BACKGROUND_BIOSYSTEM_RECORD ========== -->
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<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0">
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<TR>
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<TD class="WhiteCell ThumbText2" ALIGN="Left" VALIGN="TOP">
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<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" class="Yellow1CellBlueEdge ThumbText2">
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<TR>
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<TD ALIGN="Center" VALIGN="TOP" class="Yellow1Cell" style="white-space: nowrap;"><A HREF="#Output">OUTPUT DISPLAY</A></TD>
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</TR>
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</TABLE>
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<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" class="WhiteCellBlueEdgeBottomAndSides ThumbText2">
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<!-- TR>
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<TD ALIGN="Left" class="MicroText WhiteCell" VALIGN="TOP"> </TD>
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</TR -->
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<TR>
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<TD ALIGN="CENTER" VALIGN="TOP" style="white-space: nowrap;" class="WhiteCell">
|
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<A HREF="#Output"><IMG src="images/np_002917_cdart_thumbnail_wide.png" width="340" height="264" border=0 align="center" alt="Thumbnail image showing the domain relatives for a protein query sequence (NP_002917, regulator of G-protein signaling 12 isoform 2). Domain relatives are protein sequences that contain one or more of the conserved domains found in the query sequence. Click on the image to open the CDART help document for more information about the tool."></A>
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</TD>
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</TR>
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<!-- TR>
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<TD ALIGN="Left" class="MicroText WhiteCell" VALIGN="TOP"> </TD>
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</TR -->
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</TABLE>
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<TD class="WhiteCell ThumbText2" ALIGN="Left" VALIGN="TOP" WIDTH="10"> </TD>
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</TR>
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</TABLE>
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<BR><BR>
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<!-- ======= SINGLE_THUMBNAIL_YELLOW_BACKGROUND_HIGHLIGHT_COMPONENTS ======== -->
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<!-- TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0">
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<TR>
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<TD class="WhiteCell ThumbText2" ALIGN="Left" VALIGN="TOP">
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<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" class="Yellow1CellBlueEdge ThumbText2">
|
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<TR>
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<TD ALIGN="Center" VALIGN="TOP" class="Yellow1Cell" style="white-space: nowrap;"><A HREF="#BSSummaryHighightSelected">HIGHLIGHT SELECTED BIOSYSTEM COMPONENTS</A></TD>
|
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</TR>
|
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</TABLE>
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<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" class="WhiteCellBlueEdgeBottomAndSides ThumbText2">
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<TR>
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<TD ALIGN="Left" class="MicroText WhiteCell" VALIGN="TOP"> </TD>
|
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</TR>
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<TR>
|
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<TD ALIGN="CENTER" VALIGN="TOP" style="white-space: nowrap;" class="WhiteCell">
|
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<A HREF="#BSSummaryHighightSelected"><IMG src="images/bsid82991_ptgs1_highlighted_thumbnail.png" width="280" height="270" border=0 align="center" alt="Thumbnail image illustrating the highlight function. In this example, the PTGS1 gene, a component of the arachidonic acid metabolism pathway, is selected in the Genes folder tab of NCBI BioSystems record bsid82991 and then shown with a red outline in the full size image of that pathway on the web server of the source database, KEGG. Click on the image to read more about highlighting selected biosystem components."></A>
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</TD>
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</TR>
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</TABLE>
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<TD class="WhiteCell ThumbText2" ALIGN="Left" VALIGN="TOP" WIDTH="10"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
<BR><BR -->
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<!-- =========== ADDITIONAL_THUMBNAILS_WHITE_BACKGROUND ============== -->
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|
<!-- BR><BR>
|
|
<A HREF="#______">Thumbnail header/key concept</A><br>
|
|
<A HREF="#______"><IMG src="_________thumb.png" width="130" height="105" border=0 align="center" alt="Thumbnail image for example of ________________________. Click on image to jump to a larger, annotated version in this help document."></A>
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<BR><BR><BR>
|
|
<A HREF="#______">Thumbnail header/key concept</A><br>
|
|
<A HREF="#______"><IMG src="_________thumb.png" width="130" height="105" border=0 align="center" alt="Thumbnail image for example of ________________________. Click on image to jump to a larger, annotated version in this help document."></A>
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|
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<BR><BR><BR>
|
|
<A HREF="#______">Thumbnail header/key concept</A><br>
|
|
<A HREF="#______"><IMG src="_________thumb.png" width="130" height="105" border=0 align="center" alt="Thumbnail image for example of ________________________. Click on image to jump to a larger, annotated version in this help document."></A>
|
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|
|
<BR><BR><BR>
|
|
<A HREF="#______">Thumbnail header/key concept</A><br>
|
|
<A HREF="#______"><IMG src="_________thumb.png" width="130" height="105" border=0 align="center" alt="Thumbnail image for example of ________________________. Click on image to jump to a larger, annotated version in this help document."></A>
|
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<BR><BR -->
|
|
|
|
|
|
</TD>
|
|
</TR>
|
|
</TABLE>
|
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|
|
<!-- =========== PAGE_MARGIN_TO_RIGHT_OF_TABLE_OF_CONTENTS =============== -->
|
|
|
|
</TD>
|
|
</TR>
|
|
</TABLE>
|
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|
|
<!-- ############ END_BLUE_EDGE_BOX_WITH_TITLE_OF_DOCUMENT_AND_TOC ######## -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell NormalText"> </TD>
|
|
</TR>
|
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</TABLE>
|
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|
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<!-- ================== END_VERTICAL SPACER ===================== -->
|
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<!-- ########### BLUE_HEADER_SECTION_1_WHAT_IS_CDART ############# -->
|
|
|
|
<A NAME="WhatIs"></A>
|
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|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#F0F8FF">
|
|
<TR>
|
|
<TD class="SteelBlueCell"><SPAN class="HeaderText1">What is CDART?</SPAN></TD>
|
|
<TD class="SteelBlueCell" WIDTH="15" ALIGN="left" VALIGN="center"><A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
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<!-- ############## END_BLUE_HEADER_SECTION_1_WHAT_IS_CDART ############ -->
|
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<!-- ########## BEGIN_BLUE_EDGE_BOX_WITH_SECTION_1_CONTENTS ########### -->
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#FFFFFF">
|
|
<TR>
|
|
<TD class="WhiteCellBlueEdgeAll">
|
|
|
|
<!-- ================= LEVEL_1 ==================== -->
|
|
|
|
<A NAME="CDARTDefinition"></A>
|
|
<BR>
|
|
|
|
<P class="pad20">
|
|
The <A HREF="/Structure/lexington/lexington.cgi"><B>C</B>onserved <B>D</B>omain <B>A</B>rchitecture <B>R</B>etrieval <B>T</B>ool (<B>CDART</B>)</A> performs similarity searches of the <a HREF="/protein/">Entrez Protein</a> database based on domain architecture. A <B>domain architecture</B> is defined as the sequential order of <A HREF="../../cdd/cdd_help.shtml#CDWhat">conserved domains</A> (functional units) in a protein sequence.<BR><BR>
|
|
|
|
In this way, CDART finds protein similarities across significant evolutionary distances using sensitive domain profiles rather than direct sequence similarity.<BR><BR>
|
|
|
|
Given a query sequence, CDART shows the <A HREF="../../cdd/cdd_help.shtml#CDWhat">conserved domains</A> that make up a protein and then lists proteins with a similar domain architecture. The conserved domains in a sequence are found by <A HREF="../../cdd/cdd_help.shtml#RPSBWhat">RPS-BLAST</A>, which defines a domain by a PSSM (Position-specific scoring matrices), a set of probabilities of amino acids existing at each position of the domain. RPS-BLAST is known as a "profile" search, which is a sensitive way to look for sequence homologues. Proteins similar to the query are then grouped and scored by domain architecture.<BR><BR>
|
|
|
|
You can either <!-- A HREF="/Structure/lexington/lexington.cgi" --><A HREF="#InputCDARThomepage" -->search CDART directly</A> with a query protein sequence, <B>or</B> <!-- A HREF="/protein/" --><A HREF="#InputEntrezSearch">retrieve a protein sequence record from the Entrez Protein database</A> and select "<!-- A HREF="docs/cdd_how_to_domain_architecture.html" --><I>Domain Relatives</I>" from the "<I>Related Information</I>" menu in the right margin of the page to see the precalculated CDART results.<!-- (<A HREF="docs/cdd_how_to_domain_architecture.html"><SPAN style="color:#D70000">illustrated example</SPAN></A>) --> Relying on domain profiles allows CDART to be fast and, because it relies on annotated functional domains, informative.<BR><BR>
|
|
|
|
<B>This tool is designed for interactive use. Scripting is not supported.</B><BR><BR>
|
|
|
|
|
|
<I>(A related tool, <A HREF="/sparcle"><B>SPARCLE</B>, the <B>S</B>ubfamily <B>P</B>rotein <B>Arc</B>hitecture <B>L</B>abeling <B>E</B>ngine</A>, is a resource for the functional characterization and labeling of protein sequences that have been grouped by their characteristic conserved domain architecture. The <A HREF="../../sparcle/docs/sparcle_help.html">SPARCLE Help document</A> provides a <A HREF="../../sparcle/docs/sparcle_help.html#Compare">comparison of CDD, CDART, and SPARCLE</A> and includes examples of how each resource can be used.)</I><BR><BR>
|
|
|
|
|
|
|
|
</P>
|
|
|
|
<!-- ============== LEVEL_1_CDART_USEFUL_FEATURES ============= -->
|
|
|
|
<A NAME="DatabaseApplications"></A>
|
|
|
|
<!-- P class="indent20">
|
|
<SPAN class="HeaderText3"><B>How can CDART be used to learn more about proteins?</B></SPAN> <img SRC="/Structure/IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
|
</P>
|
|
|
|
<BLOCKQUOTE>
|
|
Text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text.
|
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<UL>
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|
|
<LI><A NAME="_____"></A><P class="pad10"><B>______________________</B></P></LI>
|
|
<UL>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
</UL>
|
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|
|
</UL>
|
|
|
|
</BLOCKQUOTE -->
|
|
|
|
<BR>
|
|
|
|
<!-- ============== END_LEVEL_1_CDART_USEFUL_FEATURES ============= -->
|
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|
|
<!-- ====== PAGE_MARGIN_TO_RIGHT_OF_BLUE_EDGE_BOX_WITH_SECTION_1_CONTENTS ====== -->
|
|
|
|
</TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ############# END_BLUE_EDGE_BOX_WITH_SECTION_1_CONTENTS ############ -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell NormalText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell MiniText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- ########### BLUE_HEADER_SECTION_2_QUICK_START ############# -->
|
|
|
|
<A NAME="QuickStart"></A>
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#F0F8FF">
|
|
<TR>
|
|
<TD class="SteelBlueCell"><SPAN class="HeaderText1">Quick Start Guide</SPAN></TD>
|
|
<TD class="SteelBlueCell" WIDTH="15" ALIGN="left" VALIGN="center"><A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ############## END_BLUE_HEADER_SECTION_2_QUICK_START ############ -->
|
|
|
|
|
|
<!-- ########## BEGIN_BLUE_EDGE_BOX_WITH_SECTION_2_CONTENTS ########### -->
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#FFFFFF">
|
|
<TR>
|
|
<TD class="WhiteCellBlueEdgeAll">
|
|
|
|
<!-- ================= LEVEL_1 ==================== -->
|
|
|
|
<A NAME="___________"></A>
|
|
<BR>
|
|
|
|
<A NAME="QuickStartPrefatoryNote"></A>
|
|
|
|
<P class="indent40">
|
|
|
|
<!-- IF LIGHT GREY BACKGROUND F5F5F5 IS USED INSTEAD OF WHITE,
|
|
CHANGE TO CELLPADDING=10 AROUND IMAGE -->
|
|
|
|
<table style="margin:0px 0px 0px 0px;" width="820" border="0" bgcolor="FFFFFF" class="NormalText" cellpadding="0">
|
|
<tr>
|
|
<td width="20" class="NormalText"> </td>
|
|
<td>
|
|
The illustration below shows the <B>easy, 1-2-3 step</B> process for using the <A HREF="/Structure/lexington/lexington.cgi"><B>C</B>onserved <B>D</B>omain <B>A</B>rchitecture <B>R</B>etrieval <B>T</B>ool (<B>CDART</B>)</A>. Click on any frame of the image below to link to subsequent sections in this help document, which provide additional details about the <A HREF="#Input">input options</A> and <A HREF="#Output">output display</A>.
|
|
</td>
|
|
</tr>
|
|
</table>
|
|
|
|
</P>
|
|
<BR><BR>
|
|
|
|
<!-- ================= QUICK_START_ILLUSTRATION ==================== -->
|
|
|
|
<A NAME="QuickStartIllustration"></A>
|
|
|
|
<!-- SINGLE IMAGE FILE; NOTE: IF LIGHT GREY BACKGROUND F5F5F5 IS USED INSTEAD OF
|
|
WHITE, CHANGE TO CELLPADDING=10 AROUND IMAGE -->
|
|
|
|
<!-- P class="indent40">
|
|
<table style="margin:0px 0px 0px 0px;" width="800" border="0" bgcolor="FFFFFF" class="NormalText" cellpadding="0">
|
|
<tr>
|
|
<td ALIGN="center">
|
|
<IMG src="images/1_2_3_proteins_to_biosystems.png" width="800" height="605" border="0" align="center" alt="Illustration of the three steps in using FLink: (1) input UIDs for desired starting database, (2) review input list and select destination database, (3) retrieve ranked list of records from destination database.">
|
|
</td>
|
|
</tr>
|
|
</table>
|
|
</P -->
|
|
|
|
<!-- SEPARATE, CLICKABLE IMAGE FILE FOR EACH PART OF GRAPHIC -->
|
|
|
|
<table style="margin:0px 0px 0px 0px;" width="820" border="0" bgcolor="FFFFFF" class="NormalText" cellpadding="0" cellspacing="0">
|
|
|
|
<tr>
|
|
|
|
<td width="20" class="NormalText"> </td>
|
|
|
|
<td width="380" ALIGN="center" VALIGN="top" class="NormalText">
|
|
<A HREF="#Input"><IMG src="images/np_002917_cdart_query_page_380_annotated.png" WIDTH="380" HEIGHT="330" border="0" align="center" alt="Illustration of the CDART home page, where you can input a query either as protein, a set of conserved domains, or as multiple queries. Click on this image for details and examples."></A>
|
|
</td>
|
|
|
|
<td width="40" ALIGN="center" VALIGN="top" class="NormalText">
|
|
<img SRC="images/about_cdart_OR_balloon.png" width="40" height="275" border="0">
|
|
</td>
|
|
|
|
<td width="380" ALIGN="center" VALIGN="top" class="NormalText">
|
|
<A HREF="#InputEntrezSearch"><IMG src="images/np_002917_link_to_domain_relatives.png" WIDTH="380" HEIGHT="330" border="0" align="center" alt="Illustration of a sample protein sequence record (regulator of G-protein signaling 12 isoform 2, NP_002917) from the Entrez Protein database, where you can follow the link for Domain Relatives to view a list of proteins with similar domain architectures. Click on this graphic to read more about the various links that exist from a protein record to conserved domains."></A>
|
|
</td>
|
|
|
|
</tr>
|
|
|
|
<tr>
|
|
|
|
<td width="20" class="NormalText"> </td>
|
|
|
|
<td width="380" ALIGN="center" class="NormalText">
|
|
<img SRC="images/about_cdart_down_arrow.png" width="40" height="25" border="0">
|
|
</td>
|
|
|
|
<td width="40" ALIGN="center" class="NormalText">
|
|
<img SRC="../../IMG/spacer.gif" width="40" height="25" border="0">
|
|
</td>
|
|
|
|
<td width="380" ALIGN="center" class="NormalText">
|
|
<img SRC="images/about_cdart_down_arrow.png" width="40" height="25" border="0">
|
|
</td>
|
|
|
|
</tr>
|
|
|
|
<tr>
|
|
<td width="20" class="NormalText"> </td>
|
|
<td colspan="3" ALIGN="center" class="NormalText">
|
|
<A HREF="#Output"><IMG src="images/np_002917_cdart_results_800.png" WIDTH="800" HEIGHT="820" border="0" align="center" alt="Illustration of CDART search results, which list proteins that have domain architectures similar to your query protein sequence (NP_002917, regulator of G-protein signaling 12 isoform 2, in this example). Click on this graphic to read more about the output display."></A>
|
|
</td>
|
|
</tr>
|
|
<!--
|
|
<tr>
|
|
<td width="20" class="NormalText"> </td>
|
|
<td colspan="3" ALIGN="left" class="NormalText">
|
|
<img SRC="../../IMG/spacer.gif" width="40" height="25" border="0">
|
|
<img SRC="images/about_cdart_down_arrow.png" width="40" height="25" border="0">
|
|
</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td width="20" class="NormalText"> </td>
|
|
<td colspan="3" ALIGN="center" class="NormalText">
|
|
<A HREF="#OutputDomainArchitecture"><IMG src="images/np_081086_cdart_results_expand_tenth_cluster.png" WIDTH="800" HEIGHT="380" border="0" align="center" alt="The expanded view of a domain architecture displays a list of representative, non-redundant protein sequences which have that architecture. Click on this graphic to read more about the information provided for each domain architecture."></A>
|
|
</td>
|
|
</tr>
|
|
-->
|
|
</table>
|
|
|
|
|
|
<!-- ================= END_QUICK_START_ILLUSTRATION ==================== -->
|
|
|
|
<!-- ================= QUICK_START_FOOTNOTE ==================== -->
|
|
|
|
<A NAME="QuickStartFootnote"></A>
|
|
|
|
<P class="indent40">
|
|
|
|
<table style="margin:0px 0px 0px 0px;" width="820" border="0" bgcolor="FFFFFF" class="NormalText" cellpadding="0">
|
|
<tr>
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<td width="20" class="NormalText"> </td>
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<td>
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<BR>
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<!-- Subsequent sections of this FLink help document provide additional details about the proper formatting of the <A HREF="#Input">input UID list</A> (part 1b of the graphic above) and the features of the <A HREF="#InputSummary">input summary display</A> (part 2a of graphic) and <A HREF="#Output">output display</A> (part 3 of graphic).<BR><BR -->
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If you would like to try this example yourself, open the <A HREF="/Structure/lexington/lexington.cgi">CDART home page</A> and enter <B>NP_002917</B> (regulator of G-protein signaling 12 isoform 2) as the query, or retrieve the <A HREF="/protein/NP_002917">sequence record from the Entrez Protein database</A> and then follow the link for "<B>Domain Relatives</B>" that appears under "Related Information" in the right margin. Click on any frame of the image above to link to subsequent sections in this help document, which provide additional details about the <A HREF="#Input">input options</A> and <A HREF="#Output">output display</A>.
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</td>
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</tr>
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</table>
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</P>
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<BR><BR>
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<!-- ================= END_QUICK_START_FOOTNOTE ==================== -->
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<!-- ====== PAGE_MARGIN_TO_RIGHT_OF_BLUE_EDGE_BOX_WITH_SECTION_2_CONTENTS ====== -->
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</TD>
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</TR>
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</TABLE>
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<!-- ############# END_BLUE_EDGE_BOX_WITH_SECTION_2_CONTENTS ############ -->
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<!-- ==================== VERTICAL SPACER ======================= -->
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<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
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<TR>
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<TD class="WhiteCell NormalText"> </TD>
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</TR>
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</TABLE>
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<!-- ================== END_VERTICAL SPACER ===================== -->
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<!-- ==================== VERTICAL SPACER ======================= -->
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<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
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<TR>
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<TD class="WhiteCell MiniText"> </TD>
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</TR>
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</TABLE>
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<!-- ================== END_VERTICAL SPACER ===================== -->
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<!-- ########### BLUE_HEADER_SECTION_3_INPUT ############# -->
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<A NAME="Input"></A>
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<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#F0F8FF">
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<TR>
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<TD class="SteelBlueCell"><SPAN class="HeaderText1">Input Options</SPAN></TD>
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<TD class="SteelBlueCell" WIDTH="15" ALIGN="left" VALIGN="center"><A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></TD>
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</TR>
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</TABLE>
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<!-- ############## END_BLUE_HEADER_SECTION_3_INPUT ############ -->
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<!-- ########## BEGIN_BLUE_EDGE_BOX_WITH_SECTION_3_CONTENTS ########### -->
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<TABLE style="margin:0px 0px 0px 0px;" class="NormalText" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#FFFFFF">
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<TR>
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<TD class="WhiteCellBlueEdgeAll">
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<!-- ============ MINI_TOC_FOR_THIS_SECTION ============== -->
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<BR>
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<BLOCKQUOTE><BLOCKQUOTE>
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| <A HREF="#InputCDARThomepage">enter query directly into CDART home page</A> as a  <A HREF="#InputProtein">protein sequence</A>, <A HREF="#InputConservedDomainSet">set of conserved domains</A>, or <A HREF="#InputMultipleQueries">multiple queries</A> |<BR>
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| <A HREF="#InputEntrezSearch">retrieve sequence record from Entrez Protein → follow "Domain Relatives" link</A> | <!-- A HREF="______">__________</A> | <A HREF="#_____">_________</A> | -->
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</BLOCKQUOTE></BLOCKQUOTE>
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<!-- ========== END_MINI_TOC_FOR_THIS_SECTION ============ -->
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<!-- ============ INPUT_OPTION_1_START_ON_CDART_HOME_PAGE ============ -->
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<A NAME="InputCDARThomepage"></A>
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<P class="indent20">
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<SPAN class="HeaderText3"><B>Enter query directly into CDART home page </B></SPAN> <img SRC="/Structure/IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
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</P>
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<BR>
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<TABLE style="margin:0px 0px 0px 0px;" class="NormalText">
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<TR>
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<TD>
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<!-- ===== IMAGE_INPUT_OPTION_1_ENTER_QUERY_DIRECTLY_INTO_CDART_HOME_PAGE ====== -->
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<IMG SRC="/Structure/IMG/spacer.gif" WIDTH="10" HEIGHT="275" BORDER="0" ALIGN="right">
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<A HREF="#QuickStart"><IMG src="images/np_002917_cdart_query_page_380_annotated.png" WIDTH="380" HEIGHT="331" border="0" align="right" alt="Illustration of the CDART home page, where you can input a query either as protein, a set of conserved domains, or as multiple queries. See the corresponding text for details and examples. Click on this image to see the complete illustration of the steps in using CDART, featured in the Quick Start Guide."></A>
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<IMG SRC="/Structure/IMG/spacer.gif" WIDTH="10" HEIGHT="275" BORDER="0" ALIGN="right">
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<!-- ==== END_IMAGE_INPUT_OPTION_1_ENTER_QUERY_DIRECTLY_INTO_CDART_HOME_PAGE ==== -->
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<!-- ============= INPUT_PROTEIN ================= -->
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<BLOCKQUOTE>
|
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One way to retrieve proteins with similar domain architectures is to enter your query as a protein sequence, or as a set of conserved domains, directly into the <A HREF="/Structure/lexington/lexington.cgi">CDART home page</A> in any of the following formats:
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</BLOCKQUOTE>
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<UL>
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<LI><A NAME="InputProtein"></A><P class="pad10"><B>Protein sequence</B> <img SRC="/Structure/IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></P></LI><BR>
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<BLOCKQUOTE>
|
|
You can submit a protein sequence as:
|
|
</BLOCKQUOTE>
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<UL>
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<LI><P class="pad10"><A NAME="InputProteinUID"></A>a <B>protein unique identifier (UID)</B> - enter the <A HREF="/Sitemap/samplerecord.html#AccessionB">Accession or GI number</A> of any protein that is in the <A HREF="/protein/">Entrez Protein</A> database.</P></LI><BR>
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<LI><P class="pad10"><A NAME="InputProteinSequence"></A><B>protein sequence data</B> - enter the sequence in <!-- A HREF="/BLAST/blastcgihelp.shtml" --><a href="https://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml">FASTA format</a> or as bare sequence data.</P></LI><BR>
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</UL>
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<BLOCKQUOTE>
|
|
The <A HREF="#Output">CDART results</A> will show the functional domains found in the query protein and will list proteins with a similar domain architecture. The similar proteins must include <B>at least one</B> of the conserved domain superfamilies in the query sequence<!--; they are not required to contain all of the domain superfamilies in the query -->. The <A HREF="#OutputDomainArchitectureSimilarityScore">similarity score</A> of each domain architecture indicates the number of domain superfamilies in the architecture that match domain superfamilies in the query protein, and is used to rank the search results.
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</BLOCKQUOTE>
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</UL>
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<!-- ============= END_INPUT_PROTEIN ================= -->
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<!-- ============= INPUT_CONSERVED_DOMAIN_SET ================= -->
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<UL>
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<LI><A NAME="InputConservedDomainSet"></A><P class="pad10"><B>Set of conserved domains (CDs)</B> <img SRC="/Structure/IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></P></LI><BR>
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<BLOCKQUOTE>As an alternative to submitting a <A HREF="#InputProtein">protein sequence</A> as a query, you can you can specify a query as a set of <B>one or more conserved domains</B><A HREF="#InputConservedDomainSetFootnote">*</A>, using <B>any of the identifiers below</B> to specify your domains of interest. They should be entered on a <B>single line</B>, separated by <B>commas</B>, and surrounded by <SPAN style="background-color: #FFFF00"><B>square brackets []</B></SPAN>, as in the examples below:<BR><BR>
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|
</BLOCKQUOTE>
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<UL>
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<LI><P class="pad10"><A NAME="InputConservedDomainSetClusterIDs"></A><B>conserved domain superfamily cluster IDs</B> - As explained in the Conserved Domain Database help document, a <A HREF="../../cdd/cdd_help.shtml#Superfamily">superfamily</A> cluster is a set of conserved domain models that generate overlapping annotation on the same protein sequences. These models are assumed to represent evolutionarily related domains and may be redundant with each other.<BR><BR>
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A superfamily ID (accession number) begins with the prefix "cl" for "cluster," and can be entered in CDART as the complete alphanumeric accession or as digits only (with or without the leading zeros). For example, a query to retrieve proteins with domain architectures that include superfamilies <A HREF="/Structure/cdd/cddsrv.cgi?uid=198498">cl00075</A> (HATPase_c Superfamily) and <A HREF="/Structure/cdd/cddsrv.cgi?uid=194440">cl02783</A> (TopoII_MutL_Trans Superfamily) can be entered in any of the following ways:<BR><BR>
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<img SRC="/Structure/IMG/spacer.gif" width="20" height="1" border="0">[cl00075,cl02783]<BR>
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<img SRC="/Structure/IMG/spacer.gif" width="20" height="1" border="0">[00075,02783]<BR>
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<img SRC="/Structure/IMG/spacer.gif" width="20" height="1" border="0">[75,2783]<BR>
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<img SRC="/Structure/IMG/spacer.gif" width="20" height="1" border="0">[cl00075,2783]<BR>
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<img SRC="/Structure/IMG/spacer.gif" width="20" height="1" border="0">etc.<BR>
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</P>
|
|
</LI><BR>
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|
|
|
<LI><P class="pad10"><A NAME="InputConservedDomainSetPSSMIDs"></A><B>Accession numbers or PSSM IDs for specific domain models</B> - If you are interested in a specific conserved domain model, you can enter its <A HREF="../../cdd/cdd_help.shtml#CDSource_accession_prefix">conserved domain accession number</A> or <A HREF="../../cdd/cdd_help.shtml#CD_PSSM">position specific scoring matrix ID (PSSM ID)</A>. If you enter a PSSM ID, <B>be sure to include a leading "p"</B> so it won't be interpreted as a cluster ID. Note: The PSSM ID is displayed in the "<A HREF="../../cdd/cdd_help.shtml#CDStatistics">Statistics</A>" box of a domain model's <A HREF="../..cdd/cdd_help.shtml#CDVisual">summary page</A> in the Conserved Domain Database. For example, a query for the domain models pfam02518 (whose current PSSM ID is 190334) and cd03483 (whose current PSSM ID is 48471) can be entered as:<BR><BR>
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<img SRC="/Structure/IMG/spacer.gif" width="20" height="1" border="0">[pfam02518,cd03483]<BR>
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<img SRC="/Structure/IMG/spacer.gif" width="20" height="1" border="0">or<BR>
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<img SRC="/Structure/IMG/spacer.gif" width="20" height="1" border="0">[p190334,p48471]<BR><BR>
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</P>
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</LI><BR>
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<LI><P class="pad10"><A NAME="InputConservedDomainSetClusterIDsAndPSSMIDs"></A><B>mix of superfamily cluster IDs, conserved domain accessions, PSSM IDs</B> - Use the same syntax rules as above. For example, a query to retrieve proteins with domain architectures that include superfamily <A HREF="/Structure/cdd/cddsrv.cgi?uid=198498">cl00075</A> and domain model <A HREF="/Structure/cdd/cddsrv.cgi?uid=cd03483">cd03483</A> (whose current PSSM ID is 48471) can be entered in any of the following ways:<BR><BR>
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<img SRC="/Structure/IMG/spacer.gif" width="20" height="1" border="0">[cl00075,cd03483]<BR>
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<img SRC="/Structure/IMG/spacer.gif" width="20" height="1" border="0">[cl00075,p48471]<BR>
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<img SRC="/Structure/IMG/spacer.gif" width="20" height="1" border="0">[00075,p48471]<BR>
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<img SRC="/Structure/IMG/spacer.gif" width="20" height="1" border="0">[75,p48471]<BR>
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<img SRC="/Structure/IMG/spacer.gif" width="20" height="1" border="0">etc.<BR>
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</P>
|
|
</LI><BR>
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</UL>
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</UL>
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|
|
<!-- ====== BOXED_FOOTNOTE_FOR_INPUT_CONSERVED_DOMAIN_SET ======= -->
|
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|
<A NAME="InputConservedDomainSetFootnote"></A>
|
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|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCell">
|
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|
|
<TR>
|
|
<TD class="WhiteCell" ALIGN="Center" VALIGN="TOP">
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="10" class="WhiteCell NormalText3">
|
|
<TR>
|
|
<TD class="WhiteCell" WIDTH="50" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
<TD class="Yellow1CellBlueEdge" ALIGN="Left" VALIGN="TOP">
|
|
<P class="indent20bottomspace NormalText3"><P class="pad10">
|
|
Note: The proteins that are returned by CDART will include <I><B>at least one</B></I> of the domains you have specified. The <A HREF="#OutputDomainArchitectureSimilarityScore">similarity score</A> of each domain architecture indicates the number of domain superfamilies in the architecture that match domain superfamilies in the query protein, and is used to rank the search results.<BR><BR>
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|
|
|
Regardless of how you specify the conserved domains in your query (as superfamily cluster IDs or as the accessions or PSSM IDs of individual domain models), the CDART <A HREF="#Output">search results</A> will display the <I><B>superfamilies</B></I> to which those models belong, and not the individual domain models themselves. However, you can see superfamilies and individual domain models by following the "domain details" link that appears in the <A HREF="#OutputDomainArchitectureExpandedView">expanded view</A> of any domain architecture.<BR><BR>
|
|
|
|
If you enter a <I><B>single conserved domain</B></I> as a query, you will retrieve all the domain architectures that contain the domain, ranked by the number of <A HREF="#OutputDomainArchitectureTotalNrSequences">non-redundant proteins</A> that have a given architecture.<BR><BR>
|
|
</P>
|
|
</TD>
|
|
<TD class="WhiteCell" WIDTH="50" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
</TD>
|
|
</TR>
|
|
|
|
</TABLE>
|
|
<BR>
|
|
|
|
<!-- ====== END_BOXED_FOOTNOTE_FOR_INPUT_CONSERVED_DOMAIN_SET ======= -->
|
|
|
|
<!-- ============= END_INPUT_CONSERVED_DOMAIN_SET ================= -->
|
|
|
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|
|
<!-- ============= INPUT_MULTIPLE_QUERIES ================= -->
|
|
|
|
<UL>
|
|
|
|
<LI><A NAME="InputMultipleQueries"></A><P class="pad10"><B>Multiple queries</B> <img SRC="/Structure/IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></P></LI><BR>
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<UL>
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|
<LI><P class="pad10">You can enter multiple queries using any of the formats above (i.e., as <A HREF="#InputProtein">protein sequences</A> or <A HREF="#InputConservedDomainSet">sets of conserved domains</A>) or a mix of those formats. Note that:<!-- Shennan, 9/13/2011: The rule to enter multiple queries are the same as for the batch CD-search initial page (they use the same parse engine), ie, ids (accession and gi) each occupy one line, FASTA or bare sequences can occupy multiple lines, etc. Cluster set like [75,2783] are considered a single-line query and must occupy one line [and must be surrounded by square brackets]. --></P></LI><BR>
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|
<UL>
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|
|
<LI>Each protein <!-- A HREF="/Sitemap/samplerecord.html#AccessionB" -->Accession or GI number<!-- /A --> should be on a separate line</LI><BR><BR>
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|
|
<LI><!-- A HREF="/BLAST/blastcgihelp.shtml" --><a href="https://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml">FASTA formatted</a> sequence data and bare sequences can occupy multiple lines. (The FASTA format definition line, however, should occupy a single line).</LI><BR><BR>
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|
|
|
<LI>If one of your queries is a <A HREF="#InputConservedDomainSet">set of conserved domains</A>, they should be entered on a single line, separated by commas, and surrounded by <SPAN style="background-color: #FFFF00"><B>square brackets []</B></SPAN>, as in the third line of the example below.</LI><BR><BR>
|
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|
|
<LI>If you include a bare sequence as one of the queries, use a blank line to separate it from the query that precedes it, as in the last part of the example below.</LI><BR><BR>
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|
|
</UL>
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|
|
<LI><P class="pad10"><A NAME="InputMultipleQueriesExample"></A><B>Example:</B> - The example below includes six queries, in the following order: (1) protein GI number; (2) protein accession number; (3) set of conserved domain superfamily cluster IDs; (4) protein sequence in FASTA format; (5) another protein sequence in FASTA format; (6) protein as bare sequence data:</P>
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|
<PRE>
|
|
269849668
|
|
EDV04934
|
|
[75,2783]
|
|
>gi|239592572|gb|EEQ75153.1| asparaginase [Ajellomyces dermatitidis SLH14081]
|
|
MSPPIPQPRQRTRSQPLFKPAVILHGGAGNIQHSRLPPELYKQYRTSLLTYLRSTTALLNADIEEEEPSI
|
|
NAKNDAVDDNMRISPASALNAAVHAVSLMEDNELFNCGRGSVFTSAGTIEMEASVMVASLLNDEDSVDDF
|
|
NNSEVNCLASEKTPGSIKRGAGVMLVRNVRHPIQLAKEVLLRTGYASDGDGDGGNMHSQLSGEYVEGLAR
|
|
DWGMEFCPDDWFWTKKRWDEHRRGLKKGKTRGRMTDGRNMGADVEVRGEGEADDGDGLYLSQGTVGCVCL
|
|
DRWGNIAVATSTGGLTNKCPGRIGDTPTLGAGFWAEAWDVEGVEGLSNMSDSSNSVCASGRDRSKGCIQL
|
|
KRDTMNYQTQDGRDNLLAYQASSSTTTTTSSYRMGSQWRSDFDSNSAFTLIRDCFSSSPPPPGYAALEPS
|
|
KYPVEKFPLGKSTSSPHTDFNPHRYSQPQRRRILALSGTGNGDSFLRTAATRTAAAMVRFGSAQNSISLA
|
|
QAVTAVAGPGGELQRSAGRRWGKTGEGEGGIIGIEAEVETDEQTLGEGKLRRGKVVFDFNSTGMFRAWME
|
|
EKDGKDVERMMVFRDDYE
|
|
>gi|336020358|ref|NP_001229488.1| mitogen-activated protein kinase kinase kinase kinase 4 isoform 4 [Homo sapiens]
|
|
MANDSPAKSLVDIDLSSLRDPAGIFELVEVVGNGTYGQVYKGRHVKTGQLAAIKVMDVTEDEEEEIKLEI
|
|
NMLKKYSHHRNIATYYGAFIKKSPPGHDDQLWLVMEFCGAGSITDLVKNTKGNTLKEDWIAYISREILRG
|
|
LAHLHIHHVIHRDIKGQNVLLTENAEVKLVDFGVSAQLDRTVGRRNTFIGTPYWMAPEVIACDENPDATY
|
|
DYRSDLWSCGITAIEMAEGAPPLCDMHPMRALFLIPRNPPPRLKSKKWSKKFFSFIEGCLVKNYMQRPST
|
|
EQLLKHPFIRDQPNERQVRIQLKDHIDRTRKKRGEKDETEYEYSGSEEEEEEVPEQEGEPSSIVNVPGES
|
|
TLRRDFLRLQQENKERSEALRRQQLLQEQQLREQEEYKRQLLAERQKRIEQQKEQRRRLEEQQRREREAR
|
|
RQQEREQRRREQEEKRRLEELERRRKEEEERRRAEEEKRRVEREQEYIRRQLEEEQRHLEVLQQQLLQEQ
|
|
AMLLECRWREMEEHRQAERLQRQLQQEQAYLLSLQHDHRRPHPQHSQQPPPPQQERSKPSFHAPEPKAHY
|
|
EPADRAREVEDRFRKTNHSSPEAQSKQTGRVLEPPVPSRSESFSNGNSESVHPALQRPAEPQVPVRTTSR
|
|
SPVLSRRDSPLQGSGQQNSQAGQRNSTSIEPRLLWERVEKLVPRPGSGSSSGSSNSGSQPGSHPGSQSGS
|
|
GERFRVRSSSKSEGSPSQRLENAVKKPEDKKEVFRPLKPADLTALAKELRAVEDVRPPHKVTDYSSSSEE
|
|
SGTTDEEDDDVEQEGADESTSGPEDTRAASSLNLSNGETESVKTMIVHDDVESEPAMTPSKEGTLIVRQT
|
|
QSASSTLQKHKSSSSFTPFIDPRLLQISPSSGTTVTSVVGFSCDGMRPEAIRQDPTRKGSVVNVNPTNTR
|
|
PQSDTPEIRKYKKRFNSEILCAALWGVNLLVGTESGLMLLDRSGQGKVYPLINRRRFQQMDVLEGLNVLV
|
|
TISGKKDKLRVYYLSWLRNKILHNDPEVEKKQGWTTVGDLEGCVHYKVVKYERIKFLVIALKSSVEVYAW
|
|
APKPYHKFMAFKSFGELVHKPLLVDLTVEEGQRLKVIYGSCAGFHAVDVDSGSVYDIYLPTHIQCSIKPH
|
|
AIIILPNTDGMELLVCYEDEGVYVNTYGRITKDVVLQWGEMPTSVAYIRSNQTMGWGEKAIEIRSVETGH
|
|
LDGVFMHKRAQRLKFLCERNDKVFFASVRSGGSSQVYFMTLGRTSLLSW
|
|
|
|
MEQDPKPPRLRLWALIPWLPRKQRPRISQTSLPVPGPGSGPQRDSDEGVLKEISITHHVKAGSEKADPSH
|
|
FELLKVLGQGSFGKVFLVRKVTRPDSGHLYAMKVLKKATLKVRDRVRTKMERDILADVNHPFVVKLHYAF
|
|
QTEGKLYLILDFLRGGDLFTRLSKEVMFTEEDVKFYLAELALGLDHLHSLGIIYRDLKPENILLDEEGHI
|
|
KLTDFGLSKEAIDHEKKAYSFCGTVEYMAPEVVNRQGHSHSADWWSYGVLMFEMLTGSLPFQGKDRKETM
|
|
TLILKAKLGMPQFLSTEAQSLLRALFKRNPANRLGSGPDGAEEIKRHVFYSTIDWNKLYRREIKPPFKPA
|
|
VAQPDDTFYFDTEFTSRTPKDSPGIPPSAGAHQLFRGFSFVATGLMEDDGKPRAPQAPLHSVVQQLHGKN
|
|
LVFSDGYVVKETIGVGSYSECKRCVHKATNMEYAVKVIDKSKRDPSEEIEILLRYGQHPNIITLKDVYDD
|
|
GKHVYLVTELMRGGELLDKILRQKFFSEREASFVLHTIGKTVEYLHSQGVVHRDLKPSNILYVDESGNPE
|
|
CLRICDFGFAKQLRAENGLLMTPCYTANFVAPEVLKRQGYDEGCDIWSLGILLYTMLAGYTPFANGPSDT
|
|
PEEILTRIGSGKFTLSGGNWNTVSETAKDLVSKMLHVDPHQRLTAKQVLQHPWVTQKDKLPQSQLSHQDL
|
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QLVKGAMAATYSALNSSKPTPQLKPIESSILAQRRVRKLPSTTL
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</PRE>
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</LI>
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</UL>
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</UL>
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</TD>
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</TR>
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</TABLE>
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<!-- ============= END_INPUT_MULTIPLE_QUERIES ================= -->
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<!-- =========== END_INPUT_OPTION_1_START_ON_CDART_HOME_PAGE =========== -->
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<!-- ============== INPUT_OPTION_2_START_IN_ENTREZ_PROTEIN ============= -->
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<A NAME="InputEntrezSearch"></A>
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<A NAME="InputEntrezProtein"></A>
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<A NAME="InputEntrezProteinDomainRelatives"></A>
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<A NAME="DomainRelatives"></A>
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<P class="indent20">
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<SPAN class="HeaderText3"><B>Search Entrez Protein → link to "Domain Relatives"</B></SPAN> <img SRC="/Structure/IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
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</P>
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<BR>
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<TABLE style="margin:0px 0px 0px 0px;" class="NormalText">
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<TR>
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<TD>
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<!-- ====== IMAGE_INPUT_OPTION_2_START_IN_ENTREZ_PROTEIN ====== -->
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<IMG SRC="/Structure/IMG/spacer.gif" WIDTH="10" HEIGHT="275" BORDER="0" ALIGN="right">
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<A HREF="#QuickStart"><IMG src="images/np_002917_link_to_domain_relatives.png" WIDTH="380" HEIGHT="330" border="0" align="right" alt="Illustration of a sample protein sequence record (regulator of G-protein signaling 12 isoform 2, NP_002917) from the Entrez Protein database, where you can follow the link for Domain Relatives to view a list of proteins with similar domain architectures. Click on this image to see the complete illustration of the steps in using CDART, featured in the Quick Start Guide."></A>
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<IMG SRC="/Structure/IMG/spacer.gif" WIDTH="10" HEIGHT="275" BORDER="0" ALIGN="right">
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<!-- ====== END_IMAGE_INPUT_OPTION_2_START_IN_ENTREZ_PROTEIN ====== -->
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<BLOCKQUOTE>
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A second way to access CDART is to start by retrieving a record of interest from the <A HREF="/protein/">Entrez Protein</A> database, then follow the "<B>Domain Relatives</B>" link in the right margin of the sequence record. That will open the precalculated <A HREF="#Output">CDART results</A> for the protein.<BR><BR>
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Note that the "Domain Relatives" is <B>one of four links</B> available from a protein sequence record to <A HREF="../../cdd/cdd_help.shtml#CDWhat">conserved domain</A> annotations, allowing you to choose:
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(a) the <B>format</B> in which you want to view the conserved domains (e.g., in <!-- A HREF="../../cdd/cdd_help.shtml#EntrezProt_LinkTo_CDDSearchResults" --><I>graphical</I> format<!-- /A --> as domain footprints aligned to the protein sequence; as a <I>list</I> of records from the <A HREF="/cdd/">Conserved Domain Database</A>, each of which includes a multiple sequence alignment of the proteins used to create the domain model; or as a list of proteins with similar <I>domain architectures</I>), and
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(b) the <B>level of redundancy</B> in the list of conserved domain models (e.g., a <!-- A HREF="______" --><I>concise</I> list of the top scoring models or a <!-- A HREF="______" --><I>full</I> list of all models that have a statistically significant <A HREF="../../cdd/cdd_help.shtml#RPSBWhat">RPS-BLAST</A> hit to the protein).<BR><BR>
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The number of conserved domain models retrieved, and the order in which they are sorted/presented, depends upon the view you select:<BR><BR>
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<!-- TABLE_WITH_ENTREZ_PROTEIN_SEQUENCE_THUMBNAIL_AND_CDD_LINK_DESCRIPTIONS -->
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<TABLE style="margin:0px 0px 0px 0px;" CLASS="NormalText" BORDER="0" CELLSPACING="0" CELLPADDING="0" BGCOLOR="#FFFFFF">
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<TR>
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<!-- ===== BRIEF_DESCRIPTIONS_OF_ENTREZ_PROTEIN_SEQUENCE_CDD_LINKS ====== -->
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<TD CLASS="NormalText" ALIGN="LEFT" VALIGN="TOP">
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<UL>
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<LI><SPAN style="color:#D70000"><A NAME="InputEntrezSearchDomainRelativesLink"></A><B>Domain Relatives</B></SPAN> -- opens a <A HREF="#Output"><B>graphical</B> display</A> of <B>similar domain architectures</B>, as determined by the <A HREF="../lexington.cgi">CDART</A> tool. <!-- Each domain architecture represents a specific set of conserved domain superfamilies in a specific order. -->A domain architecture is defined as the sequential order of conserved domains in a protein query sequence. The score for each CDART hit represents the number of domains that match those found in the query protein. (<I><!--The CDD help document -->The <A HREF="cdart_publications.html">CDART paper</A> provides <!-- A HREF="../../cdd/cdd_help.shtml#EntrezProt_LinkTo_DomainRelatives" -->additional details.</I></LI>)<BR><BR>
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<LI><SPAN style="color:#D70000">CDD Search Results</SPAN> -- opens a <B>graphical</B> display (<A HREF="../../cdd/cdd_help.shtml#ConciseDisplayIllustration">illustrated example</A>) of conserved domain model <B>footprints</B> on the query protein, ranked by their <A HREF="../../cdd/cdd_help.shtml#RPSBWhat">RPS-BLAST</A> score and <A HREF="../../cdd/cdd_help.shtml#RPSB_hit_types">hit type</A>. A model may appear <B>more than once</B> if it aligns to multiple regions of the query sequence. A concise display showing only the top-scoring hits is presented by default, and it can be changed to a full display of all hits if desired. (<I>The CDD help document provides <A HREF="../../cdd/cdd_help.shtml#EntrezProt_LinkTo_CDDSearchResults">additional details</A>.</I>)</LI><BR><BR>
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<LI><SPAN style="color:#D70000">Conserved Domains (Concise)</SPAN> -- opens a concise <B>list</B> of the conserved domain models that are the <B>top-scoring</B> <A HREF="../../cdd/cdd_help.shtml#RPSBWhat">RPS-BLAST</A> hits to the query protein. Each domain model is listed <B>only once</B>, even if a model had a hit to more than one region on the query sequence. (<I>The CDD help document provides <A HREF="../../cdd/cdd_help.shtml#EntrezProt_LinkTo_ConservedDomainsConcise">additional details</A>.</I>)</LI><BR><BR>
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<LI><SPAN style="color:#D70000">Conserved Domains (Full)</SPAN> -- opens a full <B>list</B> of <B>all</B> the conserved domain models that have a <B>statistically significant</B> <A HREF="../../cdd/cdd_help.shtml#RPSBWhat">RPS-BLAST</A> hit to the query protein. Each domain model is listed <B>only once</B>, even if a model had a hit to more than one region on the query sequence. (<I>The CDD help document provides <A HREF="../../cdd/cdd_help.shtml#EntrezProt_LinkTo_ConservedDomainsFull">additional details</A>.</I>)</LI><BR><BR>
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</UL>
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</TD>
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<!-- ===== END_BRIEF_DESCRIPTIONS_OF_ENTREZ_PROTEIN_SEQUENCE_CDD_LINKS ===== -->
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</TR>
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</TABLE>
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<!-- END_TABLE_WITH_ENTREZ_PROTEIN_SEQUENCE_THUMBNAIL_AND_CDD_LINK_DESCRIPTIONS -->
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</BLOCKQUOTE>
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</TD>
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</TR>
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</TABLE>
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<!-- ============ END_INPUT_OPTION_2_START_IN_ENTREZ_PROTEIN =========== -->
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<!-- ====== PAGE_MARGIN_TO_RIGHT_OF_BLUE_EDGE_BOX_WITH_SECTION_3_CONTENTS ====== -->
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</TD>
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</TR>
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</TABLE>
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<!-- ############# END_BLUE_EDGE_BOX_WITH_SECTION_3_CONTENTS ############ -->
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<!-- ==================== VERTICAL SPACER ======================= -->
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|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
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<TR>
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<TD class="WhiteCell NormalText"> </TD>
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</TR>
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</TABLE>
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<!-- ================== END_VERTICAL SPACER ===================== -->
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<!-- ==================== VERTICAL SPACER ======================= -->
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<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
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<TR>
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<TD class="WhiteCell MiniText"> </TD>
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</TR>
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</TABLE>
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<!-- ================== END_VERTICAL SPACER ===================== -->
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<!-- ########### BLUE_HEADER_SECTION_4_OUTPUT ############# -->
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<A NAME="Output"></A>
|
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|
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<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#F0F8FF">
|
|
<TR>
|
|
<TD class="SteelBlueCell"><SPAN class="HeaderText1">Output</SPAN></TD>
|
|
<TD class="SteelBlueCell" WIDTH="15" ALIGN="left" VALIGN="center"><A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></TD>
|
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</TR>
|
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</TABLE>
|
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|
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<!-- ############## END_BLUE_HEADER_SECTION_4_OUTPUT ############ -->
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<!-- ########## BEGIN_BLUE_EDGE_BOX_WITH_SECTION_4_CONTENTS ########### -->
|
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<TABLE style="margin:0px 0px 0px 0px;" class="NormalText" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#FFFFFF">
|
|
<TR>
|
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<TD class="WhiteCellBlueEdgeAll">
|
|
|
|
<!-- ================== OUTPUT_GRAPHICAL_SUMMARY ================ -->
|
|
|
|
<A NAME="OutputGraphicalSummary"></A>
|
|
|
|
<BR>
|
|
<P class="indent20">
|
|
<SPAN class="HeaderText3"><B>Graphical summary of similar domain architectures</B></SPAN> <img SRC="/Structure/IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
|
</P>
|
|
<BR>
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|
|
<!-- ============ MINI_TOC_FOR_THIS_SECTION ============== -->
|
|
|
|
<BLOCKQUOTE>
|
|
|
|
| <A HREF="#OutputQuery">query</A> | <A HREF="#OutputList">list of similar domain architectures</A> | <A HREF="#OutputFilters">filter your results</A> | <A HREF="#OutputDomainArchitecture">information provided for each domain architecture</A> | <!-- A HREF="______">__________</A> | <A HREF="#_____">_________</A> | -->
|
|
|
|
</BLOCKQUOTE>
|
|
|
|
<P class="indent20">When the query is successful, a graphical interface is provided for the user to navigate through the results. </P>
|
|
|
|
<!-- ========== END_MINI_TOC_FOR_THIS_SECTION ============ -->
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText">
|
|
|
|
<!-- ================== IMAGE_OUTPUT_GRAPHICAL_SUMMARY =============== -->
|
|
|
|
<TR>
|
|
<TD WIDTH="800">
|
|
<IMG SRC="/Structure/IMG/spacer.gif" WIDTH="20" HEIGHT="10" BORDER="0" ALIGN="left">
|
|
<A HREF="#QuickStart"><IMG src="images/np_002917_cdart_results_800.png" WIDTH="800" HEIGHT="820" border="0" align="center" alt="Illustration of CDART search results, which list proteins that have domain architectures similar to your query protein sequence (NP_002917, regulator of G-protein signaling 12 isoform 2, in this example). Click on this image to see the complete illustration of the steps in using CDART, featured in the Quick Start Guide."></A>
|
|
</TD>
|
|
</TR>
|
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|
|
<!-- ================== END_IMAGE_OUTPUT_GRAPHICAL_SUMMARY =============== -->
|
|
|
|
<TR>
|
|
<TD>
|
|
<BR>
|
|
<UL>
|
|
<LI><A NAME="OutputQuery"></A><P class="pad20"><B>Query</B> <img SRC="/Structure/IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></P>
|
|
<UL>
|
|
<LI><P class="pad10">The query you entered is displayed in a <B>yellow background</B> at the top of the CDART search results.</P>
|
|
<UL>
|
|
<LI><P class="pad10"><A NAME="OutputQueryProtein"></A>If your query was a <A HREF="#InputProtein">protein sequence</A>, the graphic shows the <B>length</B> of the protein in amino acids and the <B>footprints of the highest scoring conserved domain <A HREF="../../cdd/cdd_help.shtml#Superfamily">superfamily(ies)</A></B> found in the query sequence by <A HREF="../../cdd/cdd_help.shtml#RPSBWhat">RPS-BLAST</A>. On the left side of the graphic is the <B>description</B> of the query and the <B>total number of domain architectures</B> found in the Entrez Protein database that contain <B>at least one</B> superfamily from the query. If you used any <A HREF="#OutputFilters">search result filters</A>, a second number will show the number of remaining architectures after applying the filter. The two numbers may be the same.</P></LI><BR>
|
|
<LI><P class="pad10"><A NAME="OutputQueryConservedDomainSet"></A>If your query was a <A HREF="#InputConservedDomainSet">set of conserved domains</A> rather than a protein sequence, the domains will be shown in the same order in which they were input, without a scale showing length. The "total architectures" statistic will indicate the number of domain architectures found in the Entrez Protein database that contain <B>all</B> of the domain superfamilies in your query.</P></LI><BR>
|
|
</UL>
|
|
</LI><BR>
|
|
<LI><P>The <B>Download</B> button to the right of the query graph lets you download all the similar architectures found for this query (after applying the filters, if specified). Click on the button will result in a <B>Save as</B> dialog to let you save the result in a text file.</P></LI><BR>
|
|
</UL>
|
|
|
|
</LI><BR>
|
|
|
|
<LI>
|
|
<A NAME="OutputList"></A><P class="pad20"><B>List of similar domain architectures</B> <img SRC="/Structure/IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></P>
|
|
|
|
<UL>
|
|
<LI><A NAME="DomainArchitectureDefinition"></A><P class="pad10">A <B>domain architecture</B> is defined as the <B>sequential order of <A HREF="../../cdd/cdd_help.shtml#CDWhat">conserved domains</A></B> in protein queries. Each domain architecture displayed by CDART therefore represents a unique set and order of conserved domain <A HREF="../../cdd/cdd_help.shtml#Superfamily">superfamilies</A> found among sequences in the Entrez Protein database.<BR><BR></P></LI>
|
|
<LI><P class="pad10">The CDART results list the proteins with a similar domain architecture to your query. The similar proteins must include <B>at least one</B> of the conserved domain superfamilies in the query sequence. The <A HREF="#OutputDomainArchitectureSimilarityScore"><B>similarity score</B></A> of each domain architecture indicates the number of domain superfamilies in the architecture that match domain superfamilies in the query protein, and is used to rank the search results. The results are paginated at 10 architectures per page, users can nagivate to any pages using the page selector or back/forward arrows at the bottom row of the table.<BR><BR></P></LI>
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|
|
|
<LI><P class="pad10">Architectures are displayed as graphs. Different Superfamilies are displayed as <A HREF="../../cdd/cdd_help.shtml#RPSB_HitColors"><B>different shape/color combinations</B></A>. <B>Mouse over</B> a superfamily footprint to open a pop-up that shows the superfamily accession number (cluster ID), title, and description. <B>Click</B> on a footprint to open the Conserved Domain Database summary page for that superfamily, which lists the individual conserved domain models that belong to the superfamily.<BR><BR></P></LI>
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|
|
|
<LI><P class="pad10">Protein sequences that share the same domain architecture are grouped together, and only one from each group is shown. To see all proteins in the group, follow the <B>Lookup sequences in Entrez</B> link to the right of the architecture graph.<BR><BR></P></LI>
|
|
</UL>
|
|
</LI><BR>
|
|
<LI>
|
|
<A NAME="OutputFilters"></A><P class="pad20"><B>Filter your results</B> <img SRC="/Structure/IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></P>
|
|
|
|
<UL>
|
|
<LI><P class="pad10">The "<B>Filter your results</B>" bar at the top of a CDART search results page allow you to refine the results by including/excluding architectures that contain specific <B>domain superfamily(ies)</B>. The contents of the "Filter your results" dialog box are <B>generated dynamically</B> and represent the domain superfamilies that were found in your CDART search results. Select the desired superfamilies from the lists provided in the dialog box to <B>include</B> or <B>exclude</B> superfamilies from your CDART search results display.</P><BR><BR></LI>
|
|
|
|
<LI><P class="pad10">As an <B>alternative</B> to selecting domain superfamilies from the lists and then using the "Include" or "Exclude" buttons, you can <B>type the desired parameters directly into the "Filter your results" text box</B>, in a format such as:<BR><BR></P>
|
|
|
|
<UL>
|
|
<LI>
|
|
<B>INCLSFAM[xxx,yyy,zzz]</B><BR>
|
|
Include only sequences that contain the conserved domain <A HREF="../../cdd/cdd_help.shtml#Superfamily">superfamilies</A> with <A HREF="#InputConservedDomainSetClusterIDs">cluster IDs</A> xxx AND yyy AND zzz.
|
|
</LI><BR>
|
|
<LI><B>EXCLSFAM[xxx,yyy,zzz]</B><BR>
|
|
Exclude sequences that contain the conserved domain <A HREF="../../cdd/cdd_help.shtml#Superfamily">superfamilies</A> with <A HREF="#InputConservedDomainSetClusterIDs">cluster IDs</A> xxx AND yyy AND zzz.<BR><BR>
|
|
<BLOCKQUOTE>
|
|
The above operations can be combined using the <B>logical operators</B> NOT, AND and OR, as well as parentheses. For example:<BR><BR>
|
|
<B>INCLSFAM[aaa,bbb] AND NOT INCLSFAM[xxx]</B><BR><BR>
|
|
will filter your search results so they include only superfamilies aaa AND bbb, but not xxx.
|
|
<BR><BR>
|
|
The logical operators are executed with the following <B>precedence</B>:<BR><BR>
|
|
() > NOT > AND > OR
|
|
</BLOCKQUOTE><BR>
|
|
</LI><BR>
|
|
</UL>
|
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|
|
|
</LI>
|
|
</UL>
|
|
|
|
</LI><BR>
|
|
<LI><A NAME="OutputDomainArchitecture"></A><P class="pad20"><B>Information provided for each domain architecture</B> <img SRC="/Structure/IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></P>
|
|
<UL>
|
|
<LI><P class="pad10"><A NAME="OutputDomainArchitectureTitle"></A><B>Title</B> - The title of the representative protein sequence that contains this domain architecture.<BR><BR></P></LI>
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|
|
|
<LI><P class="pad10"><A NAME="OutputDomainArchitectureTaxonomicSpan"></A><B>Taxonomy span</B> - The highest taxonomic node common to all sequences with this domain architecture.<BR><BR></P></LI>
|
|
<LI>
|
|
<P class="pad10"><A NAME="OutputDomainArchitectureSimilarityScore"></A><B>Similarity score</B> - The number of conserved domain <A HREF="../../cdd/cdd_help.shtml#Superfamily">superfamilies</A> in this domain architecture that match superfamilies in the query sequence. The score does not count repeats of superfamilies within a domain architecture; rather, it counts each superfamily only once, regardless of how many times that superfamily appears in a protein sequence.<BR><BR>
|
|
The domain architectures shown on a CDART <A HREF="#Output">search results</A> page are ranked/sorted by score. If two or more architectures have the same score, they are ranked by the number of <A HREF="#OutputDomainArchitectureTotalNrSequences">non-redundant protein sequences</A> <!-- (<A HREF="#IPG">identical protein groups (IPGs)</A>) --> that contain the architecture (so hits that may be spurious hits are at the bottom).<BR><BR></P>
|
|
</LI>
|
|
<LI><P class="pad10"><A NAME="OutputDomainArchitectureTotalNrSequences"></A><B>Total nr (non-redundant) sequences</B> -</P>
|
|
<UL>
|
|
<LI>Protein sequences that share the same domain architecture are grouped together.</LI><BR>
|
|
|
|
<LI><A NAME="IPG"></A>If two or more of the proteins are identical in length and composition, they are placed in the same <SPAN style="color:#D70000"><B>identical protein group ("IPG")</B></SPAN>. CDART displays one representative sequence from each IPG in order to produce a non-redundant (nr) list of sequences that contain a specific domain architecture. To find all sequences in this group, follow the <b>Lookup sequences in Entrez</b> link</LI><BR>
|
|
|
|
<LI>The <B>"total nr sequences" statistic</B> represents the total number of IPGs with the domain architecture.</LI><BR>
|
|
</UL>
|
|
|
|
<LI><P class="pad10"><A NAME="OutputDomainArchitectureLookupSequencesInEntrez"></A><B>Lookup sequences in Entrez</B> - Retrieves the <B>non-redundant set</B> of sequence records that contain the domain architecture. The link will leave the search result page, so it is recommended to right-click on it and select to open link in a new window.<BR><BR></P></LI>
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|
|
</UL>
|
|
</LI><BR>
|
|
<LI><P class="pad20"><B>Navigate multiple queries</B> <img SRC="/Structure/IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></P></A><BR>
|
|
|
|
<P class="pad10">The graphical interface can only navigate results of one query at a time. If multiple queries have been specified, some extra controls will appear.</P><BR>
|
|
<IMG src="images/multi_cdart_results_800.png" WIDTH="100%" style="border: 1px solid #369" align="center" alt="Extra controls for multiple queries"><BR><BR>
|
|
|
|
<P class="pad10"> The <B>View Query</B> selector can be used to select to view results from a particular query. The <B>Apply to all</B> button can be used to apply a filter to results of all queries. The <B>Download All</B> button let the user download similar architectures from all queries at once. </P>
|
|
</LI><BR>
|
|
</UL>
|
|
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|
</TD>
|
|
</TR>
|
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|
|
<!-- =========== IMAGE_OUTPUT_DOMAIN_ARCHITECTURE_EXPANDED_VIEW =============== -->
|
|
<!--
|
|
<TR>
|
|
<TD WIDTH="800">
|
|
<A NAME="OutputDomainArchitectureExpandedViewIllustration"></A>
|
|
<IMG SRC="/Structure/IMG/spacer.gif" WIDTH="20" HEIGHT="10" BORDER="0" ALIGN="left">
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<TD width="18" valign="top" align="left"><A NAME="CDART_2002_GenomeRes"></A>
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<TD valign="top" align="left"><A HREF="/pubmed/12368255?dopt=AbstractPlus">Geer LY, Domrachev M, Lipman DJ, Bryant SH. CDART: protein homology by domain architecture. <B><I>Genome Res.</I> 2002</B> Oct;12(10):1619-23.</A></TD>
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<TD valign="top" align="left"><A HREF="/pubmed/_______?dopt=AbstractPlus">Authors. Article title. <B><I>Nucleic Acids Res.</I> 2010</B> Jan; VOLXX(Database issue): PXXXX-PXXX. [PubMed]</A> <A HREF="______________">[Full Text]</A></TD>
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<TD valign="top" align="left"><A HREF="/pubmed/________?dopt=AbstractPlus"><B>___DATABASENAME___ --</B> Author AB, Author AB, Author AB, Author AB, Author AB, Author AB. Title title title title title title. <B><I>JournalName</I> YYYY</B> Mmm; Vol(Issue): PPP-PPP. [PubMed]</A> <A HREF="__________">[Full Text]</A> <A HREF="/pmc/articles/_______/">[Free Author Manuscript in PubMedCentral]</A></TD>
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<TD valign="top" align="left"><A HREF="/pubmed/________?dopt=AbstractPlus"><B>___DATABASENAME___ --</B> Author AB, Author AB, Author AB, Author AB, Author AB, Author AB. Title title title title title title. <B><I>JournalName</I> YYYY</B> Mmm; Vol(Issue): PPP-PPP. [PubMed]</A> <A HREF="__________">[Full Text]</A> <A HREF="/pmc/articles/_______/">[Free Author Manuscript in PubMedCentral]</A></TD>
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<TD valign="top" align="left"><A HREF="/books/bv.fcgi?rid=handbook.chapter.ch__">Author AB, Author AB, Author AB, Author AB, Author AB, Author AB. Title title title title title title. Chapter N IN The <I><B>NCBI Handbook</B></I> [Internet], National Library of Medicine (US), National Center for Biotechnology Information, Bethesda, MD, <B>YYYY</B> Mmm. DD [revised YYYY Mmm. DD]. [cited YYYY Mmm DD]. Available from /books/bv.fcgi?rid=handbook.chapter.ch__ in Entrez Books (/books)</A>.</TD>
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<TD VALIGN="top" ALIGN="RIGHT"><SPAN CLASS="HELPBAR1" STYLE="color="#646464"">Revised 09 August 2017</SPAN></TD>
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