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5 changes: 1 addition & 4 deletions dev/Tutorial/chapter_blast.html
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the BLAST web page. We’ll just highlight a few of them here:</p>
<ul class="simple">
<li><p>The argument <code class="docutils literal notranslate"><span class="pre">url_base</span></code> sets the base URL for running BLAST over
the internet. By default it connects to the NCBI, but one can use
this to connect to an instance of NCBI BLAST running in the cloud.
Please refer to the documentation for the <code class="docutils literal notranslate"><span class="pre">qblast</span></code> function for
further details.</p></li>
the internet. By default it connects to the NCBI.</p></li>
<li><p>The <code class="docutils literal notranslate"><span class="pre">qblast</span></code> function can return the BLAST results in various
formats, which you can choose with the optional <code class="docutils literal notranslate"><span class="pre">format_type</span></code>
keyword: <code class="docutils literal notranslate"><span class="pre">&quot;XML&quot;</span></code>, <code class="docutils literal notranslate"><span class="pre">&quot;HTML&quot;</span></code>, <code class="docutils literal notranslate"><span class="pre">&quot;Text&quot;</span></code>, <code class="docutils literal notranslate"><span class="pre">&quot;XML2&quot;</span></code>, <code class="docutils literal notranslate"><span class="pre">&quot;JSON2&quot;</span></code>,
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15 changes: 5 additions & 10 deletions dev/api/Bio.Blast.NCBIWWW.html
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<dl class="py function">
<dt class="sig sig-object py" id="Bio.Blast.NCBIWWW.qblast">
<span class="sig-prename descclassname"><span class="pre">Bio.Blast.NCBIWWW.</span></span><span class="sig-name descname"><span class="pre">qblast</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">program</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">database</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sequence</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">url_base</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">NCBI_BLAST_URL</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">auto_format</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">composition_based_statistics</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">db_genetic_code</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">endpoints</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entrez_query</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'(none)'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">expect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filter</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gapcosts</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">genetic_code</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">hitlist_size</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">50</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">i_thresh</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">layout</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lcase_mask</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">matrix_name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nucl_penalty</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nucl_reward</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">other_advanced</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">perc_ident</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">phi_pattern</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">query_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">query_believe_defline</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">query_from</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">query_to</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">searchsp_eff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">service</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">threshold</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ungapped_alignment</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">word_size</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">short_query</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alignments</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">500</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alignment_view</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">descriptions</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">500</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entrez_links_new_window</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">expect_low</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">expect_high</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">format_entrez_query</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">format_object</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">format_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'XML'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_gi</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">results_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">show_overview</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">megablast</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">template_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">template_length</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">username</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'blast'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">password</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#Bio.Blast.NCBIWWW.qblast" title="Link to this definition"></a></dt>
<dd><p>BLAST search using NCBI’s QBLAST server or a cloud service provider.</p>
<dd><p>BLAST search using NCBI’s QBLAST server.</p>
<p>Supports all parameters of the old qblast API for Put and Get.</p>
<p>Please note that NCBI uses the new Common URL API for BLAST searches
on the internet (<a class="reference external" href="http://ncbi.github.io/blast-cloud/dev/api.html">http://ncbi.github.io/blast-cloud/dev/api.html</a>). Thus,
some of the parameters used by this function are not (or are no longer)
on the internet (<a class="reference external" href="https://blast.ncbi.nlm.nih.gov/doc/blast-help/urlapi.html">https://blast.ncbi.nlm.nih.gov/doc/blast-help/urlapi.html</a>).
Thus, some of the parameters used by this function are not (or are no longer)
officially supported by NCBI. Although they are still functioning, this
may change in the future.</p>
<p>The Common URL API (<a class="reference external" href="http://ncbi.github.io/blast-cloud/dev/api.html">http://ncbi.github.io/blast-cloud/dev/api.html</a>) allows
doing BLAST searches on cloud servers. To use this feature, please set
<code class="docutils literal notranslate"><span class="pre">url_base='http://host.my.cloud.service.provider.com/cgi-bin/blast.cgi'</span></code>
and <code class="docutils literal notranslate"><span class="pre">format_object='Alignment'</span></code>. For more details, please see
<a class="reference external" href="https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&amp;DOC_TYPE=CloudBlast">https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&amp;DOC_TYPE=CloudBlast</a></p>
<p>Some useful parameters:</p>
<blockquote>
<div><ul class="simple">
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<li><p>matrix_name Specify an alt. matrix (PAM30, PAM70, BLOSUM80, BLOSUM45).</p></li>
<li><p>filter “none” turns off filtering. Default no filtering</p></li>
<li><p>format_type “HTML”, “Text”, “ASN.1”, or “XML”. Def. “XML”.</p></li>
<li><p>entrez_query Entrez query to limit Blast search</p></li>
<li><p>entrez_query Entrez query to limit Blast search - only applies when searching nucleotide BLASTDBs</p></li>
<li><p>hitlist_size Number of hits to return. Default 50</p></li>
<li><p>megablast TRUE/FALSE whether to use MEga BLAST algorithm (blastn only)</p></li>
<li><dl class="simple">
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</div></blockquote>
<p>This function does no checking of the validity of the parameters
and passes the values to the server as is. More help is available at:
<a class="reference external" href="https://ncbi.github.io/blast-cloud/dev/api.html">https://ncbi.github.io/blast-cloud/dev/api.html</a></p>
<a class="reference external" href="https://blast.ncbi.nlm.nih.gov/doc/blast-help/urlapi.html">https://blast.ncbi.nlm.nih.gov/doc/blast-help/urlapi.html</a></p>
</dd></dl>

</section>
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2 changes: 1 addition & 1 deletion dev/searchindex.js
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