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<h1>CGR Impact</h1>
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</div>
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</section>
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<h2 id="how-cgr-is-improving-eukaryotic-">How CGR is improving eukaryotic research</h2>
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<h3 id="impact">Impact</h3>
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<section class="usa-section usa-grid-full" data-section="second_tier">
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<div class="usa-width-one-third mui-card mui-card--with-actions">
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<div class="mui-card-media" data-image="images/cgr/CGR_Spotlight_Bioinformatics.svg"><!-- do not remove this comment --></div>
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<div class="mui-card-content">
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<h3 id="bioinformatics-research">Bioinformatics research</h3>
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<p>Learn how resources in the NCBI Toolkit could impact discovery of new fungal pathogens in this CGR Impact Spotlight based on a published article. </p>
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</div>
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<div class="mui-card-actions">
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<p><a class="mui-button mui-button-contained" href="https://www.nlm.nih.gov/ncbi/cgr-impactspotlights/bioinformatics-PMID36124807.html">See CGR's potential impact</a></p>
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</div>
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</div>
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<div class="usa-width-one-third mui-card mui-card--with-actions">
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<div class="mui-card-media" data-image="images/cgr/CGR_Spotlight_Protein.svg"><!-- do not remove this comment --></div>
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<div class="mui-card-content">
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<h3 id="protein-evolution">Protein evolution</h3>
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<p>Find out more about the potential impact of the NCBI Toolkit on research into protein family evolution and orthology inference in our CGR Impact Spotlight based on a published article. </p>
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</div>
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<div class="mui-card-actions">
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<p><a class="mui-button mui-button-contained" href="https://www.nlm.nih.gov/ncbi/cgr-impactspotlights/protein-family-PMID26113883.html">See CGR's potential impact</a></p>
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</div>
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</div>
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<div class="usa-width-one-third mui-card mui-card--with-actions">
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<div class="mui-card-media" data-image="images/cgr/CGR_Spotlight_Cancer.svg"><!-- do not remove this comment --></div>
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<div class="mui-card-content">
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<h3 id="cancer-susceptibility">Cancer susceptibility</h3>
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<p>Check out how open-access, high-quality data from the NCBI Toolkit aided in cancer research to help predict clinical outcomes and design effective treatments.</p>
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||
</div>
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<div class="mui-card-actions">
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<p><a class="mui-button mui-button-contained" href="https://www.nlm.nih.gov/ncbi/cgr-impactspotlights/oncogene-evolution-PMID38550998.html">See CGR's impact</a></p>
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</div>
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</div>
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</section>
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<h3 id="incorporating-cgr-into-your-work">Incorporating CGR into your workflow or the classroom</h3>
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<h4 id="curricula">Curricula</h4>
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<ul>
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<li><strong><a href="https://www.nlm.nih.gov/ncbi/workshops/BioEdSummit-2024/team-projects.html?utm_source=ncbi_insights&utm_medium=referral&utm_term=bioed-summit-success-20240819">Comparative Genomics Resource (CGR) Curricula</a></strong> <ul>
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<li><strong><a href="https://github.com/NCBI-Codeathons/bioed-2024-team-carver/blob/main/Team%20Sublime%20Dynamite%20ReadMe.md">Using NCBI Tools for high school genetics investigation</a></strong>: Students that have successfully completed a majors level introductory biology course or equivalent will explore the structure and evolutionary relationships in the insulin receptor while being introduced to the genetic basis of disease. </li>
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<li><strong><a href="https://github.com/NCBI-Codeathons/bioed-2024-team-dayhoff/">Molecular basis of Insulin Receptor function using NCBI tools</a></strong>: The goal of the curriculum package is to provide a more accessible, authentic experience with actual genetic data for 9th/10th grade and AP biology students in high school.</li>
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</ul>
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</li>
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</ul>
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<h4 id="tutorials">Tutorials</h4>
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<p>Learn how to use tools in the NCBI Toolkit to support your research.</p>
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<ul>
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<li>
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<p><strong>Comparative Genomics Resource (CGR) Tutorials</strong> </p>
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<ul>
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<li><strong><a href="https://www.youtube.com/watch?v=9Meh1CV852g">CGR orthologs video tutorial</a></strong>: Learn how to identify orthologs, align the protein sequences, and explore commonalities and differences at the amino acid level.</li>
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<li><strong><a href="https://github.com/ncbi/datasets/blob/master/training/NCBI_Datasets_Orthologs.ipynb">CGR orthologs command-line tutorial</a></strong>: Learn how to use NCBI Datasets command-line tools to download protein sequnces of orthologs from certain taxa and prepare them for alignment.</li>
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</ul>
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</li>
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<li>
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<p><strong>Comparative Genome Viewer (CGV) Tutorials</strong> </p>
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<ul>
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<li><strong><a href="https://www.youtube.com/watch?v=_TA86Tu1N0c&t=1s">CGV video tutorial</a></strong>: Learn how to use CGV to view assembly-assembly alignments including cross-species alignments with this video tutorial.</li>
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<li><strong><a href="https://www.nlm.nih.gov/ncbi/workshops/2023-07_comparative-genome-viewer/demo-cgv.html">CGV written tutorial</a></strong>: Get step-by-step instructions on how to use CGV with this tutorial walking you through several case studies. </li>
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</ul>
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</li>
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<li>
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||
<p><strong><a href="https://www.ncbi.nlm.nih.gov/datasets/docs/v2/tutorials/">NCBI Datasets Tutorials</a></strong></p>
|
||
<ul>
|
||
<li><strong><a href="https://www.ncbi.nlm.nih.gov/datasets/docs/v2/tutorials/ortholog-get-one-isoform/">Find a representative protein</a></strong> : Learn how to download a single protein sequence per gene. For a given set of gene orthologs, there are often many protein sequences per gene and this in-depth tutorial demonstrates how to select and access a single representative for the gene.</li>
|
||
<li><strong><a href="https://www.ncbi.nlm.nih.gov/datasets/docs/v2/tutorials/rename-files/">Rename downloaded files</a></strong>: Find a simple script to replace a default generic file name provided by NCBI Datasets on download with a descriptive name that works for your research needs.</li>
|
||
<li><strong><a href="https://www.ncbi.nlm.nih.gov/datasets/docs/v2/tutorials/download-ortholog-dataset/">Retrieve orthology data</a></strong> : Learn to retrieve ortholog data and metadata using the NCBI Datasets command line tool in this in-depth tutorial.</li>
|
||
<li><strong><a href="https://www.ncbi.nlm.nih.gov/datasets/docs/v2/tutorials/working-with-jsonl-data-reports/">Work with JSON Lines data reports</a></strong> : Learn to work with JSON Lines data reports, NCBI Datasets format for metadata, to make them more readable, convert them to a table, and search for specific data within a report.</li>
|
||
<li><strong><a href="https://youtube.com/watch?v=8TR3OrlgtC4">Access NCBI Genome data in Galaxy</a></strong> : View our quick video guide on how to use NCBI Datasets in Galaxy to access genomic data. </li>
|
||
</ul>
|
||
</li>
|
||
<li>
|
||
<p><strong><a href="https://www.ncbi.nlm.nih.gov/datasets/docs/v2/how-tos/">NCBI Datasets Command Line Tools How-to Guides</a></strong> </p>
|
||
<ul>
|
||
<li><strong><a href="https://www.ncbi.nlm.nih.gov/datasets/docs/v2/how-tos/genes/">Retrieve gene data</a></strong> : Find example commands to get gene metadata, download a gene data package, and download an ortholog data package.</li>
|
||
<li><strong><a href="https://www.ncbi.nlm.nih.gov/datasets/docs/v2/how-tos/genomes/">Retrieve data related to genomes</a></strong>: Learn how to retrieve genomic, transcript and protein sequence, annotation and metadata for assembled genomes.</li>
|
||
<li><strong><a href="https://www.ncbi.nlm.nih.gov/datasets/docs/v2/how-tos/virus/">Retrieve data for viruses</a></strong> : View our guide on how to access virus genome sequence and metadata, including a protein data package for SARS-CoV-2. </li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<h4 id="workshops">Workshops</h4>
|
||
<p>Watch these in-depth videos to learn how to incorporate resources from the NCBI Toolkit into your comparative genomics research.</p>
|
||
<ul>
|
||
<li>
|
||
<p><strong><a href="https://www.nlm.nih.gov/ncbi/workshops/2023-07_comparative-genome-viewer/workshop-video.html">Exploring the Relationship Between Two Eukaryotic Genomes Using the Comparative Genome Viewer</a></strong>: Watch this video to learn to how compare two genomes, explore synteny, search for genes, and view pairwise alignment at the sequence level.</p>
|
||
</li>
|
||
<li>
|
||
<p><strong><a href="https://www.nlm.nih.gov/oet/ed/ncbi/2022_07_molecular.html">An Introduction to Molecular Evolutionary Analysis with NCBI Datasets and Python</a></strong>: Watch this video to learn how to compare the protein-coding sequences of two species to estimate which proteins show signs of adaptation. Working in a Jupyter notebook with bash and Python, you will use the NCBI Datasets command line interface (CLI) to download sequence data, then perform analysis with a few popular Python packages.</p>
|
||
</li>
|
||
<li>
|
||
<p><strong><a href="https://youtube.com/watch?v=C7oLXUup14E">Using NCBI Foreign Contamination Screen (FCS) to Remove Contaminants from Genome Assemblies</a></strong>: Watch this video to learn how to use FCS to remove contaminants from your genome assemblies. This video features a live demo of running FCS-GX, viewing contamination summary reports, a tour of github+wiki pages for the tool, and a question and answer session.</p>
|
||
</li>
|
||
</ul>
|
||
<h3 id="cgr-publications">CGR Publications</h3>
|
||
<p>Read all about the NIH Comparative Genomics Resource (CGR) including data and tools in the NCBI Toolkit in these free, publicly available articles</p>
|
||
<ul>
|
||
<li><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10523801/">The NIH Comparative Genomics Resource: addressing the promises and challenges of comparative genomics on human health</a></li>
|
||
<li><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10898089/">Rapid and sensitive detection of genome contamination at scale with FCS-GX</a></li>
|
||
<li><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11101090/">The NCBI Comparative Genome Viewer (CGV) is an interactive visualization tool for the analysis of whole-genome eukaryotic alignments</a></li>
|
||
<li><a href="https://https.ncbi.nlm.nih.gov/pmc/articles/PMC11226681/">Exploring and retrieving sequence and metadata for species across the tree of life with NCBI Datasets</a></li>
|
||
</ul>
|
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