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itemscope="itemscope" itemtype="http://schema.org/Article"> <div itemprop="articleBody"> <section id="common-tasks-in-bv-brc"> <h1>Common Tasks in BV-BRC<a class="headerlink" href="#common-tasks-in-bv-brc" title="Permalink to this heading">露</a></h1> <p>This page provides an overview with links to User Guides and Tutorials, organized by common tasks in BV-BRC.</p> <div class="toctree-wrapper compound"> <p class="caption" role="heading"><span class="caption-text">Contents:</span></p> <ul> <li class="toctree-l1"><a class="reference internal" href="gui_tasks.html">Common Tasks Using the Web Interface</a><ul> <li class="toctree-l2"><a class="reference internal" href="gui_tasks.html#working-with-sequences">Working with Sequences</a><ul> <li class="toctree-l3"><a class="reference internal" href="gui_tasks.html#assemble-a-set-of-reads-into-contigs">Assemble a Set of Reads into Contigs</a></li> <li class="toctree-l3"><a class="reference internal" href="gui_tasks.html#create-an-annotated-genome-from-a-set-of-contigs-and-estimate-its-quality">Create an Annotated Genome from a set of contigs and Estimate its Quality</a></li> <li class="toctree-l3"><a class="reference internal" href="gui_tasks.html#extract-as-many-complete-genomes-as-possible-from-a-meta-genomic-sample">Extract as Many Complete Genomes as Possible from a Meta-Genomic Sample</a></li> <li class="toctree-l3"><a class="reference internal" href="gui_tasks.html#annotate-a-new-genome-and-compare-it-to-similar-genomes-in-bv-brc">Annotate a New Genome and Compare it to Similar Genomes in BV_BRC</a></li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="gui_tasks.html#working-with-taxonomic-groups">Working with Taxonomic Groups</a><ul> <li class="toctree-l3"><a class="reference internal" href="gui_tasks.html#find-representative-genomes-for-a-taxon">Find Representative Genomes for a Taxon</a></li> <li class="toctree-l3"><a class="reference internal" href="gui_tasks.html#find-genomes-in-a-taxon-with-specific-attributes">Find Genomes in a Taxon with Specific Attributes</a></li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="gui_tasks.html#working-with-genomes">Working with Genomes</a><ul> <li class="toctree-l3"><a class="reference internal" href="gui_tasks.html#find-the-roles-present-in-a-genome">Find the Roles Present in a Genome</a></li> <li class="toctree-l3"><a class="reference internal" href="gui_tasks.html#compare-the-proteomes-for-a-set-of-genomes">Compare the Proteomes for a Set of Genomes</a></li> <li class="toctree-l3"><a class="reference internal" href="gui_tasks.html#visually-compare-the-protein-families-in-a-set-of-genomes">Visually Compare the Protein Families in a Set of Genomes</a></li> <li class="toctree-l3"><a class="reference internal" href="gui_tasks.html#determine-the-evidence-of-quality-for-a-genome">Determine the Evidence of Quality for a Genome</a></li> <li class="toctree-l3"><a class="reference internal" href="gui_tasks.html#find-the-closest-n-genomes-to-a-particular-genome">Find the Closest N Genomes to a Particular Genome</a></li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="gui_tasks.html#working-with-protein-families">Working with Protein Families</a><ul> <li class="toctree-l3"><a class="reference internal" href="gui_tasks.html#list-the-features-in-a-protein-family-and-the-genomes-containing-them">List the Features in a Protein Family and the Genomes Containing Them</a></li> <li class="toctree-l3"><a class="reference internal" href="gui_tasks.html#find-the-function-of-a-protein-family">Find the Function of a Protein Family</a></li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="gui_tasks.html#working-with-features">Working with Features</a><ul> <li class="toctree-l3"><a class="reference internal" href="gui_tasks.html#find-the-sequence-protein-translation-and-other-known-attributes-of-a-gene">Find the Sequence, Protein Translation, and Other Known Attributes of a Gene</a></li> <li class="toctree-l3"><a class="reference internal" href="gui_tasks.html#find-the-upstream-region-of-a-gene">Find the Upstream Region of a Gene</a></li> <li class="toctree-l3"><a class="reference internal" href="gui_tasks.html#find-all-the-genes-in-the-same-protein-family-as-a-feature">Find All the Genes in the Same Protein Family As A Feature</a></li> <li class="toctree-l3"><a class="reference internal" href="gui_tasks.html#create-an-alignment-and-the-associated-phylogenetic-tree-from-a-set-of-features">Create an Alignment and the Associated Phylogenetic Tree from a Set of Features</a></li> <li class="toctree-l3"><a class="reference internal" href="gui_tasks.html#find-the-papers-relating-to-a-specific-feature">Find the Papers Relating to a Specific Feature</a></li> </ul> </li> </ul> </li> <li class="toctree-l1"><a class="reference internal" href="../cli_tutorial/cli_common_tasks.html">Common Tasks With P3 Scripts</a><ul> <li class="toctree-l2"><a class="reference internal" href="../cli_tutorial/cli_common_tasks.html#working-with-taxonomic-groupings">Working with Taxonomic Groupings</a><ul> <li class="toctree-l3"><a class="reference internal" href="../cli_tutorial/cli_common_tasks.html#list-roles-that-are-found-in-one-species-but-not-another">List Roles that are Found in One Species but not Another</a></li> <li class="toctree-l3"><a class="reference internal" href="../cli_tutorial/cli_common_tasks.html#compute-how-many-genomes-we-have-in-a-particular-genus">Compute How Many Genomes we have in a Particular Genus</a></li> <li class="toctree-l3"><a class="reference internal" href="../cli_tutorial/cli_common_tasks.html#list-the-genomes-we-have-in-a-particular-genus">List the Genomes we have in a Particular Genus</a></li> <li class="toctree-l3"><a class="reference internal" href="../cli_tutorial/cli_common_tasks.html#compute-the-fraction-of-the-genomes-in-a-genus-that-are-resistant-to-a-particular-drug">Compute the Fraction of the Genomes in a Genus that are Resistant to a Particular Drug</a></li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="../cli_tutorial/cli_common_tasks.html#working-with-genomes">Working with Genomes</a><ul> <li class="toctree-l3"><a class="reference internal" href="../cli_tutorial/cli_common_tasks.html#find-a-genome-from-an-accession-number-or-project-id">Find a Genome from an Accession Number or Project ID</a></li> <li class="toctree-l3"><a class="reference internal" href="../cli_tutorial/cli_common_tasks.html#given-a-genome-id-find-the-name">Given a Genome ID, Find the Name</a></li> <li class="toctree-l3"><a class="reference internal" href="../cli_tutorial/cli_common_tasks.html#find-a-gene-by-name-in-a-particular-genome">Find a Gene by Name in a Particular Genome</a></li> <li class="toctree-l3"><a class="reference internal" href="../cli_tutorial/cli_common_tasks.html#display-the-cds-and-rna-features-for-a-genome-sorted-by-location-on-the-chromosome">Display the CDS and RNA features for A Genome Sorted by Location on the Chromosome</a></li> <li class="toctree-l3"><a class="reference internal" href="../cli_tutorial/cli_common_tasks.html#compute-the-upstream-regions-for-the-protein-encoding-genes-in-a-genome">Compute the Upstream Regions for the Protein-Encoding Genes in a Genome</a></li> <li class="toctree-l3"><a class="reference internal" href="../cli_tutorial/cli_common_tasks.html#compute-the-codon-usage-in-a-genome">Compute the Codon Usage in a Genome</a></li> <li class="toctree-l3"><a class="reference internal" href="../cli_tutorial/cli_common_tasks.html#extract-a-fasta-file-of-a-genome-s-contigs">Extract a Fasta File of a Genome鈥檚 Contigs</a></li> <li class="toctree-l3"><a class="reference internal" href="../cli_tutorial/cli_common_tasks.html#list-the-protein-sequences-for-the-genes-in-a-genome">List the Protein Sequences for the Genes in a Genome</a></li> <li class="toctree-l3"><a class="reference internal" href="../cli_tutorial/cli_common_tasks.html#given-a-list-of-genomes-produce-a-list-of-pairs-of-roles-that-are-implemented-by-genes-that-are-close-on-the-chromosome-sorted-by-number-of-occurrences">Given a List of Genomes, Produce a List of Pairs of Roles that are Implemented by Genes that are Close on the Chromosome, Sorted by Number of Occurrences</a></li> <li class="toctree-l3"><a class="reference internal" href="../cli_tutorial/cli_common_tasks.html#extract-the-genomes-in-a-list-that-have-gc-content-values-greater-than-a-certain-percentage">Extract the Genomes in a List that have GC Content Values Greater Than a Certain Percentage</a></li> <li class="toctree-l3"><a class="reference internal" href="../cli_tutorial/cli_common_tasks.html#compute-how-close-two-features-are-on-the-chromosome">Compute how Close Two Features are on the Chromosome</a></li> <li class="toctree-l3"><a class="reference internal" href="../cli_tutorial/cli_common_tasks.html#list-the-drugs-to-which-a-genome-is-resistant">List the Drugs to which a Genome is Resistant</a></li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="../cli_tutorial/cli_common_tasks.html#working-with-anti-microbial-drugs">Working with Anti-Microbial Drugs</a><ul> <li class="toctree-l3"><a class="reference internal" href="../cli_tutorial/cli_common_tasks.html#find-genomes-that-are-resistant-to-a-particular-drug">Find Genomes that are Resistant to a Particular Drug</a></li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="../cli_tutorial/cli_common_tasks.html#working-with-protein-families">Working with Protein Families</a><ul> <li class="toctree-l3"><a class="reference internal" href="../cli_tutorial/cli_common_tasks.html#compute-the-average-length-of-proteins-in-a-particular-family">Compute the Average Length of Proteins in A Particular Family</a></li> <li class="toctree-l3"><a class="reference internal" href="../cli_tutorial/cli_common_tasks.html#list-the-genome-and-feature-id-for-each-feature-in-a-protein-family">List the Genome and Feature ID for Each Feature in a Protein Family</a></li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="../cli_tutorial/cli_common_tasks.html#working-with-features">Working with Features</a><ul> <li class="toctree-l3"><a class="reference internal" href="../cli_tutorial/cli_common_tasks.html#find-the-global-protein-family-containing-a-particular-feature">Find the Global Protein Family Containing a Particular Feature</a></li> <li class="toctree-l3"><a class="reference internal" href="../cli_tutorial/cli_common_tasks.html#find-the-function-a-particular-feature-implements">Find the Function a Particular Feature implements</a></li> <li class="toctree-l3"><a class="reference internal" href="../cli_tutorial/cli_common_tasks.html#find-a-feature-from-an-alternate-feature-id">Find a Feature from an Alternate Feature ID</a></li> <li class="toctree-l3"><a class="reference internal" href="../cli_tutorial/cli_common_tasks.html#given-a-feature-id-find-the-amino-acid-sequence">Given a Feature ID, Find the Amino Acid Sequence</a></li> <li class="toctree-l3"><a class="reference internal" href="../cli_tutorial/cli_common_tasks.html#find-how-many-genomes-have-an-identical-protein-to-a-given-feature">Find How many Genomes have an Identical Protein to a Given Feature</a></li> <li class="toctree-l3"><a class="reference internal" href="../cli_tutorial/cli_common_tasks.html#given-a-feature-id-find-the-features-in-the-same-protein-family">Given a Feature ID, Find the Features in the Same Protein Family</a></li> </ul> </li> </ul> </li> </ul> </div> </section> </div> </div> <footer> <hr/> <div 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