403 lines
25 KiB
HTML
403 lines
25 KiB
HTML
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<a class="lf" href="cobalt.cgi?CMD=Web">COBALT</a> <span id="brc">Constraint-based Multiple Alignment Tool</span>
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<li class="first active"><a href="cobalt.cgi?CMD=Web">Home</a></li>
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<div id="content-wrap">
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<!--<span class="pgt">Cobalt Constraint-based Multiple Protein Alignment Tool</span>-->
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<div id="content">
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<!-- Do errors this way -->
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<ul id="msg" class="msg"><li class=""></li></ul>
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<form name="searchForm" enctype="multipart/form-data" action="cobalt.cgi?CMD=submit" method="post" class="f-wrap-1" id="searchForm" >
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<!-- <FORM name="searchForm" action="?request=page&seqList=true&seqType=Protein&submitRequest=on&dispAlignsID=0" method=post class="f-wrap-1" id="searchForm" > -->
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<div id="progDescr">
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COBALT computes a multiple protein sequence alignment using conserved domain and local sequence similarity information.
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<a href="#" title="help" class="helplink showing" id="moreHelp"><span>[?]</span></a>
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</div>
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<div id="pagelinks"><a href="#" id="resetlink" resetform="searchForm">Reset page</a></div>
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<div class="helpbox hidden" id="mhlp" toggle="moreHelp">
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COBALT is a multiple sequence alignment tool that finds a collection of pairwise constraints derived from conserved domain database, protein motif database, and sequence similarity, using RPS-BLAST, BLASTP, and PHI-BLAST.
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<br />
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Pairwise constraints are then incorporated into a progressive multiple alignment.
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<br />
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More details in <a href="https://www.ncbi.nlm.nih.gov/pubmed/17332019">Papadopoulos JS and Agarwala R,
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Bioinformatics 23:1073-79, 2007 (PMID: 17332019)</a>
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</div>
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<div id="query" class="section">
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<fieldset class="section">
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<legend>Enter Query Sequences</legend>
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<div class="qs">
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<div class="formblock all" id="qseq">
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<label for="seq">Enter at least 2 protein accessions, gis, or FASTA sequences</label>
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<a class="helplink hiding" title="help" href="#" id="queryHelp"><span>[?]</span></a>
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<a href="#" class="clearlink" fieldToClear="seq" id="clearseq">Clear</a>
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<div toggle="queryHelp" class="helpbox hidden" id="hq">
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Query sequences to be aligned should be pasted in the text area.
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It automatically determines the format or the input. To allow this feature there
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are certain conventions required with regard to the input of identifiers.
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<a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=BlastHelp" target="helpWin" class="helplink">more...</a>
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</div>
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<textarea id="seq" class="reset" rows="6" cols="96" name="seqsToAlignFastA" ></textarea>
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<br />
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<label for="upl" class="m" >Or, upload FASTA file</label>
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<div class="input ">
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<input type="file" id="upl" name="fileSeqsToAlignFastA" />
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</div>
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<label for="jt" class="m" >Job Title</label>
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<div class="input ">
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<input type="text" id="jt" size="63" value="" name="jobTitle" />
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</div>
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</div> <!-- qseq -->
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</div><!-- /.qs -->
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</fieldset>
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</div> <!-- query -->
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<div class="searchInfo ">
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<div class="summary">
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<img border="0" id="b1" src="css/images/align.jpg" class="alnbutton" alt="Align" mouseovImg="css/images/alignOver.jpg" mouseoutImg="css/images/align.jpg" mousedownImg="css/images/alignDown.jpg" mouseupImg="css/images/alignOver.jpg" />
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<div class="searchsummary">
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<div class="openNewWin ">
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<input class="newwin" type="checkbox" name="NEWWIN" id="nw1" form="searchForm" winType="random" />
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<label class="inlineLabel " for="nw1">Show results in a new window</label>
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</div>
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</div>
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</div>
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<div class="" id="optSection">
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<div id="sopts" class="section">
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<a href="#i" class="arrowlink hiding moreOptions" id="toggleOptions">Advanced parameters</a>
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<div id="moreopts" toggle="toggleOptions" class="hidden">
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<fieldset class="section">
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<legend>Alignment Parameters</legend>
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<label for="GOP" class="m ">Gap Penalties</label>
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<div class="input ">
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<div class=" infl">
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<label for="GOP">Opening</label>
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<label for="GEP" class="lbLm">Extension</label>
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</div>
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<input name="gapOpenPenalty" id="GOP" type="text" size="5" value="-11" />
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<input name="gapExtendPenalty" id="GEP" type="text" size="5" value="-1" class="rs" />
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<a class="helplink" title="help" href="#" id="gopHelp"><span>[?]</span></a>
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<p toggle="gopHelp" class="helpbox hidden">
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Gap opening penalty and gap extension penalty for gaps inside of a sequence used in pairwise global alignment
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in the progressive alignment stage.
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</p>
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</div>
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<label for="EGOP" class="m ">End-Gap Penalties</label>
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<div class="input ">
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<div class=" infl">
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<label for="EGOP">Opening</label>
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<label for="EGEP" class="lbLm">Extension</label>
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</div>
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<input name="endGapOpenPenalty" id="EGOP" type="text" size="5" value="-5" />
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<input name="endGapExtendPenalty" id="EGEP" type="text" size="5" value="-1" class="rs" />
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<a class="helplink" title="help" href="#" id="egopHelp"><span>[?]</span></a>
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<p toggle="egopHelp" class="helpbox hidden">
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Gap opening penalty and gap extension penalty for gaps at ends of a sequence used in pairwise global alignment
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in the progressive alignment stage.
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</p>
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</div>
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</fieldset>
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<fieldset class="section">
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<legend>Constraint Parameters</legend>
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<label for="URB" class="m ">RPS blast</label>
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<div class="input">
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<input name="useRPSBlast" type="checkbox" checked="checked" class="reset" id="URB" />
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<label class="right inlinelabel" for="URB">Use RPS BLAST to guide alignment</label>
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<a class="helplink" title="help" href="#" id="urbHelp"><span>[?]</span></a>
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<p toggle="urbHelp" class="helpbox hidden">
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Use RPS-BLAST to find conserved domains in query sequences to guide alignment. The sequence matches to conserved
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domains will be converted into pair wise alignment constraints. Ranges of input sequences that match to the same
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conserved domain will be aligned to each other in the final multiple alignment. We strongly recommend checking
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this box. <br />
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This box can be unchecked in order to decrease computation time if all sequences are expected to match to the
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same conserved domains or not to match to any conserved domain. COBALT is optimized for cases where groups of
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sequences do match to the same domain (see <i>Query Clustering</i> below). <br />
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<b>Note:</b> Unchecking this box in other cases will result in poorer alignment.
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</p>
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</div>
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<label for="BE" class="m ">Constraint E-value</label>
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<div class="input ">
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<input name="blastEvalue" id="BE" type="text" size="5" value="0.005" />
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<a class="helplink" title="help" href="#" id="beHelp"><span>[?]</span></a>
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<p toggle="beHelp" class="helpbox hidden">
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E-value threshold for accepting BLAST-P hits in pair wise local alignment of input sequences. The accepted
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matches will be converted into pair wise alignment constraints. Pair wise locally aligned ranges of input
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sequences will be aligned to one another in the multiple alignment. E-value can be increased if very dissimilar
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sequences are used. <br />
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<b>Note:</b> Changing this value can significantly impact quality of the resulting alignment.
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</p>
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</div>
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<label for="FCC" class="m ">Conserved columns</label>
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<div class="input">
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<input name="findConservedCols" type="checkbox" checked="checked" class="reset" id="FCC" />
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<label class="right inlinelabel" for="FCC">Find Conserved Columns and Recompute Alignment</label>
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<a class="helplink" title="help" href="#" id="fccHelp"><span>[?]</span></a>
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<p toggle="fccHelp" class="helpbox hidden">
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Identify conserved columns after the first iteration of progressive alignment and re-align input sequences using
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this information. Unchecking this box will reduce computation time but will also result in poorer alignment
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(especially if <i>Use query clusters</i> box is checked). We strongly recommend checking this box.
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</p>
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</div>
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</fieldset>
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<fieldset class="section">
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<legend>Query Clustering Parameters</legend>
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<label for="UQC" class="m ">Query Clustering Parameters</label>
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<div class="input">
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<input name="useQueryClusters" type="checkbox" checked="checked" class="reset" id="UQC" />
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<label class="right inlinelabel" for="UQC">Use query clusters</label>
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<a class="helplink" title="help" href="#" id="uqcHelp"><span>[?]</span></a>
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<p toggle="uqcHelp" class="helpbox hidden">
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Reduce computation time by using clusters of similar sequences. The idea behind using clusters is that constraints
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do not contribute information for alignment of very similar sequences. Then computationally intensive tasks
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of identifying conserved domains and consistent set of constraints can be avoided for many sequences. Clusters of
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similar sequences are found using alignment-free k-mer counting-based method. See Edgar RC, <i>Nucleic Acids Res</i>
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16:380-5, 2004, <i>PMID: 14729922</i> for k-mer counting-based sequence similarity.
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Constraints will be computed only for cluster representatives. In-cluster sequences will be aligned using combined
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local and global alignment. We recommend that the <i>Find Conserved Columns and Recompute Alignment</i> option (above) is
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also selected.
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We recommend using this option for aligning BLAST results and whenever a subset of input sequences that
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share conserved domains is expected.
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This option can be unchecked for aligning of sequences that are not expected to share conserved domains and are
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expected to have very short pair wise local alignments.
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</p>
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</div>
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<label for="WS" class="m ">Word Size</label>
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<div class="input ">
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<select name="wordSize" id="WS">
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<option value="3" >3</option>
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<option value="4" selected="selected" >4</option>
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<option value="5" >5</option>
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<option value="6" >6</option>
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<option value="7" >7</option>
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</select>
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<a class="helplink" title="help" href="#" id="wsHelp"><span>[?]</span></a>
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<p toggle="wsHelp" class="helpbox hidden">
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Number of letters in a word (k-mer) for k-mer count-based sequence similarity computation. Smaller words will
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make sequences more similar than larger words.
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</p>
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</div>
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<label for="MCD" class="m ">Max Cluster distance</label>
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<div class="input ">
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<select name="maxClusterDist" id="MCD">
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<option value="0.6" >0.6</option>
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<option value="0.65" >0.65</option>
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<option value="0.7" >0.7</option>
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<option value="0.75" >0.75</option>
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<option value="0.8" selected="selected" >0.8</option>
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<option value="0.85" >0.85</option>
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<option value="0.9" >0.9</option>
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<option value="0.95" >0.95</option>
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</select>
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<a class="helplink" title="help" href="#" id="mcdHelp"><span>[?]</span></a>
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<p toggle="mcdHelp" class="helpbox hidden">
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Maximum allowed distance between two sequences in a cluster. This threshold prvents COBALT from forming clusters
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o unrelated sequences.
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The distance between two sequences is computed as a fraction of words that appear in both sequences with respect
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to number of all words in the longer sequence (similarly as in Edgar RC, <i>Nucleic Acids Res</i>
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16:380-5, 2004, <i>PMID: 14729922</i>).
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This distance overestimates exponentially scaled percentage of different residues in aligned sequences (see graphs
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in the above paper for details).
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Allowed range for this threshold is between 0 and 1. Smaller values result in more clusters and hence more
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conserved domain-based constraints used in multiple alignment. Larger values result in fewer clusters and
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hence less conserved domain information used in multiple alignment.
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</p>
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</div>
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<label for="ALPH" class="m ">Alphabet</label>
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<div class="input ">
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<select name="alphabet" id="ALPH" class="reset">
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<option value="2" selected="selected" >SE-B15</option>
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<option value="1" >SE-V10</option>
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<option value="0" >Regular</option>
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</select>
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<a class="helplink" title="help" href="#" id="alphHelp"><span>[?]</span></a>
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<div toggle="alphHelp" class="helpbox hidden">
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Alphabet for creating k-mer count representations of sequences.
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Available options:
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<ul>
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<li>SE-B15 and SE-V10 - 15 and 10-letter compressed alphabets (see Shiryev SA et al.,
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Bioinformatics 23:2949-51, 2007, <i>PMID: 17921491</i> for details)</li>
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<li>Regular - regular 20-amino-acid alphabet.</li>
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</ul>
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</div>
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</div>
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</fieldset>
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<div class="searchInfo ">
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<div class="summary">
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<img border="0" id="b2" src="css/images/align.jpg" class="alnbutton" alt="Align" mouseovImg="css/images/alignOver.jpg" mouseoutImg="css/images/align.jpg" mousedownImg="css/images/alignDown.jpg" mouseupImg="css/images/alignOver.jpg" />
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</div>
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<div class="searchsummary">
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<div class="openNewWin ">
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<input class="newwin" type="checkbox" name="NEWWIN" id="nw2" form="searchForm" winType="random" />
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<label class="inlineLabel " for="nw2">Show results in a new window</label>
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</div>
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</div>
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</div>
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</div><!-- moreopts -->
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</div>
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</div>
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<input name="distanceMethod" value="0" type="hidden" />
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<!-- <input name="inputScreen" value="true" type="hidden" />
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<input name="AlignSeqs" value="" id="AlignSeqs" type="hidden" /> -->
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<input name="link_loc" type="hidden" value="cobaltInpPage"/>
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</form>
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