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<h1 id="how-to">How To</h1>
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<p>These are links to demonstrate how to access the NCBI Pathogen Detection data
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for some of the analysis tasks you might want to do. For more details see <a href="/pathogens/pathogens_help/">our
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documentation</a>. The How To's are meant to
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generalizable to answer other questions. If you have suggestions for changes or
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other How To's you think would be useful please set us know at
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<a href="mailto:pd-help@ncbi.nlm.nih.gov">pd-help@ncbi.nlm.nih.gov</a>.</p>
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<h4 id="visual-how-tos">Visual How Tos</h4>
|
||
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<ul>
|
||
<li><a href="/core/assets/pathogens/files/HowTo/find_an_isolate_you_submitted.pdf">How To: Find an isolate you submitted</a>
|
||
(<a href="/core/assets/pathogens/files/HowTo/find_an_isolate_you_submitted.pptx">.pptx</a>)</li>
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<li><a href="/core/assets/pathogens/files/HowTo/latestSalmonellaisolatesv1.pdf">How To: Find the latest Salmonella in the Isolates Browser</a>
|
||
(<a href="/core/assets/pathogens/files/HowTo/latestSalmonellaisolatesv1.pptx">.pptx</a>)</li>
|
||
<li><a href="/core/assets/pathogens/files/HowTo/DownloadEfclinical_v1.pdf">How To: Download a list of human, clinical <em>E. faecailis</em> isolates</a>
|
||
(<a href="/core/assets/pathogens/files/HowTo/DownloadEfclinical_v1.pptx">.pptx</a>)</li>
|
||
<li><a href="/core/assets/pathogens/files/HowTo/identifyisolateswithcontigswithsharedgenesv1.pdf">How To: Identify isolates in the same SNP cluster that share a set of genes</a>
|
||
(<a href="/core/assets/pathogens/files/HowTo/identifyisolateswithcontigswithsharedgenesv1.pptx">.pptx</a>)</li>
|
||
<li><a href="/core/assets/pathogens/files/HowTo/download_list_of_carbapenemases.pdf">How To: Download a list of all carbapenem resistance genes and point mutations from the Reference Gene Catalog</a>
|
||
(<a href="/core/assets/pathogens/files/HowTo/download_list_of_carbapenemases.pptx">.pptx</a>)</li>
|
||
<li><a href="/core/assets/pathogens/files/HowTo/allaac6primeoneBvariantsv1.pdf">How To: Download all the reference sequences for a set of proteins</a>
|
||
(<a href="/core/assets/pathogens/files/HowTo/allaac6primeoneBvariantsv1.pptx">.pptx</a>)</li>
|
||
<li><a href="/core/assets/pathogens/files/HowTo/allknownresistancemechanismtoadrugv1.pdf">How To: Find all the known resistance mechanisms to a given drug</a>
|
||
(<a href="/core/assets/pathogens/files/HowTo/allknownresistancemechanismtoadrugv1.pptx">.pptx</a>)</li>
|
||
<li><a href="/core/assets/pathogens/files/HowTo/Download_MCR-1nucleotideseqv1.pdf">How To: Download the nucleotide sequence of all MCR-1 alleles</a>
|
||
(<a href="/core/assets/pathogens/files/HowTo/Download_MCR-1nucleotideseqv1.pptx">.pptx</a>)</li>
|
||
<li><a href="/core/assets/pathogens/files/HowTo/identifycontigswithsharedgenesv1.pdf">How To: Identify all the contigs that share a set of genes</a>
|
||
(<a href="/core/assets/pathogens/files/HowTo/identifycontigswithsharedgenesv1.pptx">.pptx</a>)</li>
|
||
<li><a href="/core/assets/pathogens/files/HowTo/identifyisolateswithcontigswithsharedgenesv1.pdf">How To: Identify isolates that have a pair of genes on the same contig</a>
|
||
(<a href="/core/assets/pathogens/files/HowTo/identifyisolateswithcontigswithsharedgenesv1.pptx">.pptx</a>)</li>
|
||
<li><a href="/core/assets/pathogens/files/HowTo/download_microbigge_table.pdf">How To: Download a MicroBIGG-E table > 100,000 rows (all CARBAPENEM genes found in Pathogen Detection isolate assemblies)</a>
|
||
(<a href="/core/assets/pathogens/files/HowTo/download_microbigge_table.pptx">.pptx</a>)</li>
|
||
<li><a href="/core/assets/pathogens/files/HowTo/how_to_cite_pathogen_detection.pdf">How To: Cite the Pathogen Detection Resource and the Data Contained Within</a>
|
||
(<a href="/core/assets/pathogens/files/HowTo/how_to_cite_pathogen_detection.pptx">.pptx</a>)</li>
|
||
<li><a href="/core/assets/pathogens/files/HowTo/search_ast_data.pdf">How To: Identify carbapenem-resistant isolates without common acquired carbapenem resistance genes</a>
|
||
(<a href="/core/assets/pathogens/files/HowTo/search_ast_data.pptx">.pptx</a>) </li>
|
||
<li><a href="/core/assets/pathogens/files/HowTo/findisolatesinbrowserwithMicrobiggemap.pdf">How To: Find, using the MicroBIGG-E Map, <em>blaKPC</em>-containing <em>Klebsiella pneumoniae</em> isolates from China and the U.S. in the Isolates Browser</a>
|
||
(<a href="/core/assets/pathogens/files/HowTo/findisolatesinbrowserwithMicrobiggemap.pptx">.pptx</a>) </li>
|
||
<li><a href="/core/assets/pathogens/files/HowTo/downloadsequencesinMicrobiggeusingmapselection.pdf">How To: Download, using the MicroBIGG-E Map, <em>blaKPC</em> nucleotide sequences from <em>Klebsiella pneumoniae</em> isolates from China and the U.S.</a>
|
||
(<a href="/core/assets/pathogens/files/HowTo/downloadsequencesinMicrobiggeusingmapselection.pptx">.pptx</a>)</li>
|
||
<li><a href="/core/assets/pathogens/files/HowTo/watch_an_isolate_not_in_a_cluster.pdf">How To: Watch an isolate not in a cluster</a>
|
||
(<a href="/core/assets/pathogens/files/HowTo/watch_an_isolate_not_in_a_cluster.pptx">.pptx</a>)</li>
|
||
<li><a href="/core/assets/pathogens/files/HowTo/FindIMIresisbasedonMICv2.pdf">How To: Identify imipenem non-susceptible <em>E. cloacae</em> isolates based on MIC values and view them in the Isolates Browser</a>
|
||
(<a href="/core/assets/pathogens/files/HowTo/FindIMIresisbasedonMICv2.pptx">.pptx</a>)</li>
|
||
<li><a href="/core/assets/pathogens/files/HowTo/FindIMIresisbasedondiskv2.pdf">How To: Identify imipenem non-susceptible E. coli isolates based on disk diffusion values and view them in the MicroBIGG-E</a>
|
||
(<a href="/core/assets/pathogens/files/HowTo/FindIMIresisbasedondiskv2.pptx">.pptx</a>)</li>
|
||
</ul>
|
||
|
||
<h4 id="other-how-tos">Other How Tos</h4>
|
||
|
||
<ul>
|
||
<li><a href="/pathogens/pathogens_help/#how-to-quick-link-searches">Isolates Browser How To: Quick link searches</a></li>
|
||
<li><a href="/pathogens/pathogens_help/#how-to-general-text-searches">Isolates Browser How To: General text searches</a></li>
|
||
<li><a href="/pathogens/pathogens_help/#how-to-field-specific-searches">Isolates Browser How To: Field-specific searches</a></li>
|
||
<li><a href="/pathogens/pathogens_help/#how-to-facet-search-results">Isolates Browser How To: Use filters to focus search results</a></li>
|
||
<li><a href="/pathogens/pathogens_help/#how-to-outbreak">Isolates Browser How To: Identify the possible source of an outbreak</a></li>
|
||
<li><a href="/pathogens/submit-data/">How to submit data</a></li>
|
||
<li><a href="/pathogens/submit-beta-lactamase/">How to submit new beta-lactamase alleles</a></li>
|
||
</ul>
|
||
|
||
</div>
|
||
|
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|
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