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<dt class="hidden db">Database</dt><dd class="hidden db">nr</dd>
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<dt class="hidden entrez">Entrez Query</dt><dd class="hidden entrez"><span class="note entrez">Note: Your search is limited to records matching this Entrez query</span></dd>
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<dt>Format<br/>
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<dd>
<table class="options blastx ">
<tr class="paramSet xgl">
<td class="hd"><label for="FORMAT_OBJECT">Show</label></td>
<td>
<div class="fi">
<select id="FORMAT_OBJECT" class="reset" name="FORMAT_OBJECT" defVal="Alignment">
<option value="Alignment" >Alignment</option>
<option value="PSSM_Scoremat" >PssmWithParameters</option>
<option value="Bioseq" >Bioseq</option>
</select>
<label for="FORMAT_TYPE">as</label>
<select name="FORMAT_TYPE" id="FORMAT_TYPE" class="reset" defVal="HTML">
<option value="HTML" >HTML</option>
<option value="Text" >Plain text</option>
<option value="ASN.1" >ASN.1</option>
<option value="XML" >XML</option>
</select>
<input name="PSSM_FORMAT_TYPE" value="Text" size="3" id="pssmFormat" type="text" class="hidden dispType" />
<input name="BIOSEQ_FORMAT_TYPE" value="ASN.1" size="3" id="bioseqFormat" type="text" class="hidden dispType" />
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</span>
<a class="resetAll" id="resetAll" >Reset form to defaults</a>
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="Alignments object formatting help" id="formatHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
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<p class="helpbox ui-ncbitoggler-slave" id="hlp1">
These options control formatting of alignments in results pages. The
default is HTML, but other formats (including plain text) are available.
PSSM and PssmWithParameters are representations of Position Specific Scoring Matrices and are only available for PSI-BLAST.
The Advanced view option allows the database descriptions to be sorted by various indices in a table.
<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#format_object" target="helpWin" title="Additional alignments object formatting help">more...</a>
</p>
</div><!-- ARIA -->
</div>
</td>
</tr>
<tr class="odd paramSet">
<td class="hd"><label for="ALIGNMENT_VIEW">Alignment View</label></td>
<td>
<div class="fi">
<select name="ALIGNMENT_VIEW" id="ALIGNMENT_VIEW" defVal="Pairwise" class="reset">
<option value="Pairwise" >Pairwise</option>
<option value="PairwiseWithIdentities" >Pairwise with dots for identities</option>
<option value="QueryAnchored" >Query-anchored with dots for identities</option>
<option value="QueryAnchoredNoIdentities" >Query-anchored with letters for identities</option>
<option value="FlatQueryAnchored" >Flat query-anchored with dots for identities</option>
<option value="FlatQueryAnchoredNoIdentities" >Flat query-anchored with letters for identities</option>
<option value="Tabular" >Hit Table</option>
</select>
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="Alignments view options help" id="alnViewHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
<span class="ui-icon ui-icon-triangle-1-e"></span></a>
<div class="ui-helper-reset" aria-live="assertive" >
<p class="helpbox ui-ncbitoggler-slave" id="hlp2">
Choose how to view alignments.
The default "pairwise" view shows how each subject sequence aligns
individually to the query sequence. The "query-anchored" view shows how
all subject sequences align to the query sequence. For each view type,
you can choose to show "identities" (matching residues) as letters or
dots.
<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#alignment_view" target="helpWin" title="Additional alignments view options help">more...</a>
</p>
</div><!-- ARIA -->
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</td>
</tr>
<tr class="paramSet">
<td class="hd"><label>Display</label></td>
<td class="cb">
<div class="fi">
<input name="SHOW_OVERVIEW" id="SHOW_OVERVIEW" type="checkbox" class="cb reset" defVal="checked" checked="checked" />
<label class="rb" for="SHOW_OVERVIEW">Graphical Overview</label>
<span id="shl" >
<input name="SHOW_LINKOUT" id="SHOW_LINKOUT" type="checkbox" class="cb reset" defVal="checked" checked="checked" />
<label class="rb" for="SHOW_LINKOUT">Linkout</label>
</span>
<span id="gts" >
<input name="GET_SEQUENCE" id="GET_SEQUENCE" type="checkbox" class="cb reset" defVal="checked" checked="checked" />
<label class="rb" for="GET_SEQUENCE">Sequence Retrieval</label>
</span>
<input name="NCBI_GI" id="NCBI_GI" type="checkbox" class="cb reset" defVal="unchecked" />
<label class="rb" for="NCBI_GI">NCBI-gi</label>
<span id="scf" >
<input name="SHOW_CDS_FEATURE" id="SHOW_CDS_FEATURE" type="checkbox" class="cb reset blastn" defVal="unchecked" />
<label for="SHOW_CDS_FEATURE" class="blastn">CDS feature</label>
</span>
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="Alignments display options help" id="displayHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
<span class="ui-icon ui-icon-triangle-1-e"></span></a>
<div class="ui-helper-reset" aria-live="assertive" >
<ul class="helpbox ui-ncbitoggler-slave" id="hlp3">
<li>Graphical Overview: Graphical Overview: Show graph of similar sequence regions aligned to query.
<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#show_overview" target="helpWin" title="Graphical Overview help">more...</a>
</li>
<li>Database LinkOuts: Show links from matching sequences to entries in specialized NCBI databases.
<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#show_linkout" title="LinkOut help" target="helpWin" >more...</a>
</li>
<li>Sequence Retrieval: Show buttons to download matching sequences.
<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#get_sequence" title="Sequence Retrieval help" target="helpWin" >more...</a>
</li>
<li>NCBI-gi: Show NCBI gi identifiers.
<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#ncbi_gi" title="NCBI-gi help" target="helpWin" >more...</a>
</li>
<li>CDS feature: Show annotated coding region and translation.
<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#show_cds_feature" title="CDS feature help" target="helpWin" >more...</a>
</li></ul>
</div><!-- ARIA -->
</div>
</td>
</tr>
<tr class="paramSet odd xgl">
<td class="hd"><label>Masking</label></td>
<td>
<div class="fi">
<label for="MASK_CHAR"> Character: </label>
<select name="MASK_CHAR" id="MASK_CHAR" class="reset" defVal="2">
<option value="0" >X for protein, n for nucleotide</option>
<option value="2" selected="selected" >Lower Case</option>
</select>
<label for="MASK_COLOR"> Color:</label>
<select name="MASK_COLOR" id="MASK_COLOR" class="reset" defVal="1">
<option value="0" >Black
</option>
<option value="1" selected="selected" >Grey
</option>
<option value="2" >Red
</option>
</select>
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="Alignments masking help" id="maskingHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
<span class="ui-icon ui-icon-triangle-1-e"></span></a>
<div class="ui-helper-reset" aria-live="assertive" >
<ul class="helpbox ui-ncbitoggler-slave" id="hlp4">
<li>Masking Character: Display masked (filtered) sequence regions as lower-case or as specific letters (N for nucleotide, P for protein).
</li>
<li>Masking Color: Display masked sequence regions in the given color.</li>
</ul>
</div><!-- ARIA -->
</div>
</td>
</tr>
<tr id="lr" class="paramSet xgl">
<td class="hd"><label>Limit results</label></td>
<td>
<div class="fi">
<label for="FRM_DESCRIPTIONS">Descriptions:</label>
<select name="DESCRIPTIONS" id="FRM_DESCRIPTIONS" class="reset" defVal="100">
<option value="0" >0</option>
<option value="10" >10</option>
<option value="50" >50</option>
<option value="100" selected="selected" >100</option>
<option value="250" >250</option>
<option value="500" >500</option>
<option value="1000" >1000</option>
<option value="5000" >5000</option>
<option value="10000" >10000</option>
<option value="20000" >20000</option>
</select>
<label for="FRM_NUM_OVERVIEW">Graphical overview:</label>
<select name="NUM_OVERVIEW" id="FRM_NUM_OVERVIEW" class="reset" defVal="100">
<option value="0" >0</option>
<option value="10" >10</option>
<option value="50" >50</option>
<option value="100" selected="selected" >100</option>
<option value="250" >250</option>
<option value="500" >500</option>
<option value="1000" >1000</option>
</select>
<span id="frmAln">
<label for="FRM_ALIGNMENTS">Alignments:</label>
<select name="ALIGNMENTS" id="FRM_ALIGNMENTS" class="reset" defVal="100">
<option value="0" >0</option>
<option value="10" >10</option>
<option value="50" >50</option>
<option value="100" selected="selected" >100</option>
<option value="250" >250</option>
<option value="500" >500</option>
<option value="1000" >1000</option>
<option value="5000" >5000</option>
<option value="10000" >10000</option>
<option value="20000" >20000</option>
</select>
</span>
<label for="FRM_LINE_LENGTH">Line length:</label>
<select name="LINE_LENGTH" id="FRM_LINE_LENGTH" class="reset" defVal="60">
<option value="60" >60</option>
<option value="90" >90</option>
<option value="120" >120</option>
<option value="150" >150</option>
</select>
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="Limit number of descriptions/alignments help" id="numHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
<span class="ui-icon ui-icon-triangle-1-e"></span></a>
<div class="ui-helper-reset" aria-live="assertive" >
<ul class="helpbox ui-ncbitoggler-slave" id="hlp5">
<li>Descriptions: Show short descriptions for up to the given number of sequences.</li>
<li>Alignments: Show alignments for up to the given number of sequences, in order of statistical significance.</li>
<li>Line lenghth: ....</li>
</ul>
</div><!-- ARIA -->
</div>
</td>
</tr>
<tr class="paramSet odd xgl ">
<td class="hd"></td>
<td>
<div class="">
<label for="qorganism">Organism</label>
<span class="instr">Type common name, binomial, taxid, or group name. Only 20 top taxa will be shown.</span><br>
<input name="FORMAT_ORGANISM" size="55" type="text" id="qorganism" value="" data-jigconfig="dictionary:'taxids_sg'" autocomplete="off" class="jig-ncbiautocomplete reset">
<input type="checkbox" name="FORMAT_ORG_EXCLUDE" class="oExclR cb" id="orgExcl"/>
<input type="hidden" value = "1" name="FORMAT_NUM_ORG" id="numOrg" />
<label for="orgExcl" class="right">Exclude</label>
<a href="#" title="Add organism" id="addOrg"><img border="0" src="css/images/addOrg.jpg" id="addOrgIm" alt="Add organism" mouseovImg="css/images/addOrgOver.jpg" mouseoutImg="css/images/addOrg.jpg" mousedownImg="css/images/addOrgDown.jpg" mouseupImg="css/images/addOrgOver.jpg" /></a>
<div id="orgs">
</div>
<div class="fi">
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="Limit results by organism help" id="organismHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
<span class="ui-icon ui-icon-triangle-1-e"></span></a>
<div class="ui-helper-reset" aria-live="assertive" >
<p class="helpbox ui-ncbitoggler-slave" id="hlp6">
Show only sequences from the given organism.
</p>
</div><!-- ARIA -->
</div>
</div>
</td>
</tr>
<tr class="paramSet xgl ">
<td class="hd"></td>
<td>
<div class="fi">
<label for="FORMAT_EQ_TEXT">Entrez query:</label>
<input name="FORMAT_EQ_TEXT" id="FORMAT_EQ_TEXT" size="60" type="text" value="" class="reset" />
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="Limit results by Entrez query help" id="entrezHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
<span class="ui-icon ui-icon-triangle-1-e"></span></a>
<div class="ui-helper-reset" aria-live="assertive" >
<p class="helpbox ui-ncbitoggler-slave" id="hlp7">
Show only those sequences that match the given Entrez query.
<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#limit_result" target="helpWin" title="Additional limit results by Entrez query help" target="helpWin">more...</a>
</p>
</div><!-- ARIA -->
</div>
</td>
</tr>
<tr class="paramSet odd xgl">
<td class="hd"></td>
<td>
<div class="fi">
<label for="EXPECT_LOW">Expect Min:</label> <input name="EXPECT_LOW" id="EXPECT_LOW" size="10" type="text" value="" class="reset"/>
<label for="EXPECT_HIGH">Expect Max:</label> <input name="EXPECT_HIGH" id="EXPECT_HIGH" size="10" type="text" value="" class="reset" />
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="Limit results by expect value range help" id="expectHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
<span class="ui-icon ui-icon-triangle-1-e"></span></a>
<div class="ui-helper-reset" aria-live="assertive" >
<p class="helpbox ui-ncbitoggler-slave" id="hlp8">
Show only sequences with expect values in the given range.
<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#expect_range" target="helpWin" title="Additional limit results by expect value range help">more...</a>
</p>
</div><!-- ARIA -->
</div>
</td>
</tr>
<tr class="paramSet xgl">
<td class="hd"></td>
<td>
<div class="fi">
<label for="PERC_IDENT_LOW">Percent Identity Min:</label> <input name="PERC_IDENT_LOW" id="PERC_IDENT_LOW" size="10" type="text" value="" class="reset"/>
<label for="PERC_IDENT_HIGH">Percent Identity Max:</label> <input name="PERC_IDENT_HIGH" id="PERC_IDENT_HIGH" size="10" type="text" value="" class="reset" />
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="Limit results by percent identity range help" id="percIdentHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
<span class="ui-icon ui-icon-triangle-1-e"></span></a>
<div class="ui-helper-reset" aria-live="assertive" >
<p class="helpbox ui-ncbitoggler-slave" id="hlp10">
Show only sequences with percent identity values in the given range.
</p>
</div><!-- ARIA -->
</div>
</td>
</tr>
<tr class="psiBlast odd paramSet xgl">
<td class="hd"><label>Format for</label></td>
<td>
<div class="fi">
<input name="RUN_PSIBLAST_FORM" id="RUN_PSIBLAST" type="checkbox" class="cb psiBlast" />
<label class="rb psiBlast" for="RUN_PSIBLAST">PSI-BLAST</label>
<label for="I_THRESH">with inclusion threshold:</label>
<input name="I_THRESH" id="I_THRESH" size="10" type="text" value="" defVal="0.005" />
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="PSI BLAST formatting help" id="psiHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
<span class="ui-icon ui-icon-triangle-1-e"></span></a>
<div class="ui-helper-reset" aria-live="assertive" >
<ul class="helpbox ui-ncbitoggler-slave" id="hlp9">
<li>Format for PSI-BLAST: The Position-Specific Iterated BLAST (PSI-BLAST) program performs iterative searches with a protein query,
in which sequences found in one round of search are used to build a custom score model for the next round.
<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#psiblast" target="helpWin" title="Additional PSI BLAST formatting help">more...</a>
</li>
<li>Inclusion Threshold: This sets the statistical significance threshold for including a sequence in the model used
by PSI-BLAST to create the PSSM on the next iteration.</li>
</ul>
</div><!-- ARIA -->
</div>
</td>
</tr>
</table>
</dd>
</dl>
<input name="RID" value="" type="hidden" />
<input name="CDD_RID" value="" type="hidden" />
<input name="CDD_SEARCH_STATE" type="hidden" value="" />
<input name="STEP_NUMBER" value="" id="stepNumber" type="hidden" />
<input name="CMD" value="Get" type="hidden" />
<input name="FORMAT_EQ_OP" value="AND" type="hidden" />
<input name="RESULTS_PAGE_TARGET" type="hidden" id="resPageTarget" value="Blast_Results_for_741411994" />
<input name="QUERY_INFO" type="hidden" value="" />
<input name="ENTREZ_QUERY" type="hidden" value="" />
<input name="QUERY_INDEX" type="hidden" value="0"/>
<input name="NUM_QUERIES" type="hidden" value="1"/>
<input name="CONFIG_DESCR" type="hidden" value="2,3,4,5,6,7,8" />
<!-- Those params are set in the template (blastn.dat, blastp.dat etc. -->
<input name="BLAST_PROGRAMS" type="hidden" value="blastx"/>
<input name="PAGE" type="hidden" value="Translations"/>
<input name="PROGRAM" type="hidden" value="blastx"/>
<input name="MEGABLAST" type="hidden" value="" />
<input name="RUN_PSIBLAST" type="hidden" value="" />
<input name="BLAST_SPEC" id="blastSpec" type="hidden" value=""/>
<input name="QUERY" type="hidden" value=""/>
<input name="JOB_TITLE" type="hidden" value=""/>
<input name="QUERY_TO" type="hidden" value=""/>
<input name="QUERY_FROM" type="hidden" value=""/>
<input name="EQ_TEXT" type="hidden" value=""/>
<input name="ORGN" type="hidden" value=""/>
<input name="EQ_MENU" type="hidden" value=""/>
<input name="ORG_EXCLUDE" type="hidden" value=""/>
<input name="PHI_PATTERN" type="hidden" value=""/>
<input name="EXPECT" type="hidden" value="1e-07"/>
<input name="DATABASE" type="hidden" value="nr"/>
<input name="DB_GROUP" type="hidden" value=""/>
<input name="SUBGROUP_NAME" type="hidden" value=""/>
<input name="GENETIC_CODE" type="hidden" value=""/>
<input name="WORD_SIZE" type="hidden" value=""/>
<input name="MATCH_SCORES" type="hidden" value=""/>
<input name="MATRIX_NAME" type="hidden" value=""/>
<input name="GAPCOSTS" type="hidden" value=""/>
<input name="MAX_NUM_SEQ" id="maxNumSeq" type="hidden" value=""/>
<input name="COMPOSITION_BASED_STATISTICS" type="hidden" value=""/>
<input name="NEWWIN" type="hidden" value=""/>
<input name="SHORT_QUERY_ADJUST" type="hidden" value=""/>
<input name="FILTER" type="hidden" value=""/>
<input name="REPEATS" type="hidden" value=""/>
<input name="ID_FOR_PSSM" type="hidden" value=""/>
<input name="EXCLUDE_MODELS" type="hidden" value=""/>
<input name="EXCLUDE_SEQ_UNCULT" type="hidden" value=""/>
<input name="WP_PROTEINS" type="hidden" value=""/>
<input name="SEQ_FROM_TYPE" type="hidden" value=""/>
<input name="ENTREZ_QUERY" type="hidden" value=""/>
<input name="ENTREZ_QUERY_PRESET" type="hidden" value=""/>
<input name="ENTREZ_QUERY_PRESET_EXCL" type="hidden" value=""/>
<input name="NUM_ORG" type="hidden" value = "1" />
<!-- PSSM -->
<input name="LCASE_MASK" type="hidden" value=""/>
<input name="TEMPLATE_TYPE" type="hidden" value=""/>
<input name="TEMPLATE_LENGTH" type="hidden" value=""/>
<input name="I_THRESH" type="hidden" value=""/>
<input name="PSI_PSEUDOCOUNT" type="hidden" value=""/>
<input name="DI_THRESH" type="hidden" id="diThresh" value=""/>
<input name="HSP_RANGE_MAX" type="hidden" value=""/>
<input name="ADJUSTED_FOR_SHORT_QUERY" type="hidden" value=""/>
<input name="MIXED_QUERIES" type="hidden" value=""/>
<input name="MIXED_DATABASE" id="mixedDb" type="hidden" value=""/>
<input name="BUILD_NAME" type="hidden" value=""/>
<input name="ORG_DBS" type="hidden" value=""/>
<!--QBlastInfoBegin
RID =
RTOE =
QBlastInfoEnd
-->
</form>
</div><!-- /#content -->
</div><!-- /#content-wrap -->
<div id="footer">
<div id="rgs">BLAST is a registered trademark of the National Library of Medicine.</div>
<p id="orgns">
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</p>
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