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<meta name="robots" content="NOINDEX,NOFOLLOW,NOARCHIVE,NOIMAGEINDEX" /><meta name="citation_inbook_title" content="SRA Knowledge Base [Internet]" /><meta name="citation_title" content="Searching for Species-Specific Data" /><meta name="citation_publisher" content="National Center for Biotechnology Information (US)" /><meta name="citation_date" content="2014/03/18" /><meta name="citation_fulltext_html_url" content="https://www.ncbi.nlm.nih.gov/books/NBK569236/" /><link rel="schema.DC" href="http://purl.org/DC/elements/1.0/" /><meta name="DC.Title" content="Searching for Species-Specific Data" /><meta name="DC.Type" content="Text" /><meta name="DC.Publisher" content="National Center for Biotechnology Information (US)" /><meta name="DC.Date" content="2014/03/18" /><meta name="DC.Identifier" content="https://www.ncbi.nlm.nih.gov/books/NBK569236/" /><meta name="og:title" content="Searching for Species-Specific Data" /><meta name="og:type" content="book" /><meta name="og:url" content="https://www.ncbi.nlm.nih.gov/books/NBK569236/" /><meta name="og:site_name" content="NCBI Bookshelf" /><meta name="og:image" content="https://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcgifs/bookshelf/thumbs/th-helpsrakb-lrg.png" /><meta name="twitter:card" content="summary" /><meta name="twitter:site" content="@ncbibooks" /><meta name="warning" content="This publication is provided for historical reference only and the information may be out of date." /><meta name="bk-non-canon-loc" content="/books/n/helpsrakb/srch_SpeciesSpecif/" /><link rel="canonical" href="https://www.ncbi.nlm.nih.gov/books/NBK569236/" /><link rel="stylesheet" href="/corehtml/pmc/css/figpopup.css" type="text/css" media="screen" /><link rel="stylesheet" href="/corehtml/pmc/css/bookshelf/2.26/css/books.min.css" type="text/css" /><link rel="stylesheet" href="/corehtml/pmc/css/bookshelf/2.26/css/books_print.min.css" type="text/css" /><style type="text/css">p a.figpopup{display:inline !important} .bk_tt {font-family: monospace} .first-line-outdent .bk_ref {display: inline} </style><script type="text/javascript" src="/corehtml/pmc/js/jquery.hoverIntent.min.js"> </script><script type="text/javascript" src="/corehtml/pmc/js/common.min.js?_=3.18"> </script><script type="text/javascript">window.name="mainwindow";</script><script type="text/javascript" src="/corehtml/pmc/js/bookshelf/2.26/book-toc.min.js"> </script><script type="text/javascript" src="/corehtml/pmc/js/bookshelf/2.26/books.min.js"> </script>
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<div class="pre-content"><div><div class="bk_prnt"><p class="small">NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.</p><p>SRA Knowledge Base [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2011-. </p></div><div class="messagearea bk_noprnt" style="margin-bottom:1.3846em "><ul class="messages"><li class="warn icon"><span class="icon">This publication is provided for historical reference only and the information may be out of date.</span></li></ul></div><div class="bk_prnt"><p style="color:red;"><strong>This publication is provided for historical reference only and the information may be out of date.</strong></p></div></div></div>
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<div class="main-content lit-style" itemscope="itemscope" itemtype="http://schema.org/CreativeWork"><div class="meta-content fm-sec"><h1 id="_NBK569236_"><span class="title" itemprop="name">Searching for Species-Specific Data</span></h1><p class="small">Created: <span itemprop="datePublished">August 22, 2011</span>; Last Update: <span itemprop="dateModified">March 18, 2014</span>.</p><p><em>Estimated reading time: 2 minutes</em></p></div><div class="body-content whole_rhythm" itemprop="text"><ul class="simple-list"><li><p><a href="#srch_SpeciesSpecif.how_do_i_find_sra_dat">How do I find SRA data for African strains of fruit fly using Entrez SRA?</a></p></li><li><p><a href="#srch_SpeciesSpecif.how_do_i_find_sra_dat_1">How do I find SRA data for African strains of fruit fly using the “Object Search” tab on the SRA home page?</a></p></li><li><p><a href="#srch_SpeciesSpecif.how_do_i_find_sra_ent">How do I find SRA entries for sequenced complete genomes of the Euryarchaeota group of archaea?</a></p></li></ul><div><h4 id="srch_SpeciesSpecif.how_do_i_find_sra_dat">How do I find SRA data for African strains of fruit fly using Entrez SRA?</h4><blockquote><p>Enter the search phrase <span class="bk_pgobj">fruit fly AND Africa</span> or <span class="bk_pgobj">Drosophila AND Africa</span> into the <a href="/sra" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Entrez SRA</a> search box, and click the “search” button.</p><ul><li class="half_rhythm"><div>You can make your search more specific by using Entrez search limits. Click the “<a href="/sra/limits" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Limit</a>” link to specify a value for any or all of the following:</div><ul><li class="half_rhythm"><div>Publication date</div></li><li class="half_rhythm"><div>Search Field Tags</div></li><li class="half_rhythm"><div>Access level</div></li><li class="half_rhythm"><div>Date Modified</div></li><li class="half_rhythm"><div>Molecule</div></li><li class="half_rhythm"><div>Availability of loadable data</div></li></ul></li></ul><p>Once you have specified your limits, click the “Search” button on the Limit page to apply your limits to the search terms you entered in the search box at the top of the page.</p><ul><li class="half_rhythm"><div>You can also make your search more specific by using the Entrez “Advanced” search. Click the “<a href="/sra/advanced" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Advanced</a>” link to go to the SRA Advanced Search page, which contains:</div><ul><li class="half_rhythm"><div>“Search Builder”<br />This tool helps you select search fields and field values to create a search statement that reflects your specific search requirements.</div></li><li class="half_rhythm"><div>“Search History”<br />This tool keeps a record of up to 100 searches and their results so that you do not duplicate searches and can combine previous searches for more specificity.</div></li></ul></li><li class="half_rhythm"><div>For help using Entrez “Limits” or “Advanced” search options, see the <a href="/books/n/helpentrez/EntrezHelp/#EntrezHelp.Entrez__the_Life_Sci">Entrez Help documentation</a>.</div></li></ul><p><b>Note:</b> Since SRA is a raw data archive (not curated) and can index only those terms that a submitter provides in the metadata of their submission, your search results may not include all possible studies associated with your search term.</p></blockquote></div><div><h4 id="srch_SpeciesSpecif.how_do_i_find_sra_dat_1">How do I find SRA data for African strains of fruit fly using the “Object Search” tab on the SRA home page?</h4><blockquote><p>Enter the search phrase <span class="bk_pgobj">fruit fly AND Africa</span> or <span class="bk_pgobj">Drosophila AND Africa</span> into the “<a href="http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=search_obj" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Search for SRA related objects</a>” search box, and click the “search” button. You can use any Entrez search statement in SRA’s “Search for related objects”, but this search page does not have the “Limit” and “Advanced” search <a href="/books/NBK569236/#srch_SpeciesSpecif.how_do_i_find_sra_dat_1">features</a> that the <a href="/sra/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Entrez SRA</a> search has.</p><p><b>Note:</b> Since SRA is a raw data archive (not curated) and can index only those terms that a submitter provides in the metadata of their submission, your search results may not include all possible studies associated with your search term.</p></blockquote></div><div><h4 id="srch_SpeciesSpecif.how_do_i_find_sra_ent">How do I find SRA entries for sequenced complete genomes of the Euryarchaeota group of archaea?</h4><blockquote><dl class="temp-labeled-list"><dt>1.</dt><dd><p class="no_top_margin">Go to the <a href="/taxonomy" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Entrez Taxonomy</a> page.</p></dd><dt>2.</dt><dd><p class="no_top_margin">Enter <span class="bk_pgobj">Euryarchaeota[organism] AND taxonomy_sra[filter]</span> in the search box at the top of the page.</p></dd><dt>3.</dt><dd><p class="no_top_margin">Click the “Search” button.</p></dd><dt>4.</dt><dd><p class="no_top_margin">The response page provides you with a list of the organisms in this phylum that have published SRA sequencing.</p></dd><dt>5.</dt><dd><p class="no_top_margin">Click the organism of interest to go to the Taxonomy Browser page for that organism.</p></dd><dt>6.</dt><dd><p class="no_top_margin">Click on the link for “SRA Experiments” under “Entrez Records” for this organism to go to the SRA database.</p></dd><dt>7.</dt><dd><p class="no_top_margin">You will see a list of experiments (<a href="/books/n/helpsrakb/srch_Understand_SRA/#srch_Understand_SRA.what_do_the_differen">SRX/ERX/DRX</a> accessions).</p></dd><dt>8.</dt><dd><p class="no_top_margin">Click on the SRX record of interest. The record will include:</p><dl class="temp-labeled-list"><dt>a.</dt><dd><p class="no_top_margin">Links to each run in the experiment</p></dd><dt>b.</dt><dd><p class="no_top_margin">Experiment design information</p></dd><dt>c.</dt><dd><p class="no_top_margin">Submission accession and submitter name</p></dd><dt>d.</dt><dd><p class="no_top_margin">Study summary and abstract (if available)</p></dd><dt>e.</dt><dd><p class="no_top_margin">Experiment sample (SRS) information</p></dd><dt>f.</dt><dd><p class="no_top_margin">Links to a list of experiments (SRX)</p></dd><dt>g.</dt><dd><p class="no_top_margin">Library information (if available)</p></dd><dt>h.</dt><dd><p class="no_top_margin">Platform information</p></dd><dt>i.</dt><dd><p class="no_top_margin">Processing information (base calls and quality scores)</p></dd><dt>j.</dt><dd><p class="no_top_margin">Spot descriptor information</p></dd><dt>k.</dt><dd><p class="no_top_margin">Links to related information</p></dd></dl></dd><dt>9.</dt><dd><p class="no_top_margin">At this point, you can do one of the following:</p><dl class="temp-labeled-list"><dt>a.</dt><dd><p class="no_top_margin"><b>Click on the “All experiments” link</b> for a complete list of the experiments included in the study.</p></dd><dt>b.</dt><dd><p class="no_top_margin"><b>Download the data for a particular experiment</b> by clicking on the SRA or the SRA-lite download links. These links will take you to the SRA FTP site where the files are available for download. If there are no download links in the experiment record, please contact <a href="mailto:dev@null" data-email="vog.hin.mln.ibcn@ars" class="oemail">vog.hin.mln.ibcn@ars</a>.</p></dd><dt>c.</dt><dd><p class="no_top_margin"><b>Click on one of the</b>
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<a href="/books/n/helpsrakb/srch_Understand_SRA/#srch_Understand_SRA.each_srx_entry_in_th"><b>run links</b></a>
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<b>(</b><a href="/books/n/helpsrakb/srch_Understand_SRA/#srch_Understand_SRA.what_do_the_differen">SRR/ERR/DRR</a>
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<b>accessions)</b> to go to the SRA Run Browser, where you can look at individual reads, search the spots for a specific sequence, or download a set of spots from the run.</p></dd></dl></dd></dl><p><b>Note:</b> Since SRA is a raw data archive (not curated) and can index only those terms that a submitter provides in the metadata of their submission, your search results may not include all possible studies associated with your search term.</p><p><b>Note</b>: If you choose to download files, install the “<a href="http://www.asperasoft.com/download_connect/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Aspera Connect</a>” plug-in to transfer files at a significantly faster rate than ftp.</p></blockquote></div><div id="bk_toc_contnr"></div></div></div>
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<div class="post-content"><div><div class="half_rhythm"><a href="/books/about/copyright/">Copyright Notice</a></div><div class="small"><span class="label">Bookshelf ID: NBK569236</span></div><div style="margin-top:2em" class="bk_noprnt"><a class="bk_cntns" href="/books/n/helpsrakb/">Contents</a><div class="pagination bk_noprnt"><a class="active page_link prev" href="/books/n/helpsrakb/search/" title="Previous page in this title">< Prev</a><a class="active page_link next" href="/books/n/helpsrakb/srch_SpecifStudType/" title="Next page in this title">Next ></a></div></div></div></div>
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