CGR Impact

Incorporating CGR into your workflow or the classroom

Curricula

• Comparative Genomics Resource (CGR) Curricula
  • Using NCBI Tools for high school genetics investigation: 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.
  • Molecular basis of Insulin Receptor function using NCBI tools: 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.

Tutorials

Learn how to use tools in the NCBI Toolkit to support your research.

• Comparative Genomics Resource (CGR) Tutorials

  • CGR orthologs video tutorial: Learn how to identify orthologs, align the protein sequences, and explore commonalities and differences at the amino acid level.
  • CGR orthologs command-line tutorial: Learn how to use NCBI Datasets command-line tools to download protein sequnces of orthologs from certain taxa and prepare them for alignment.

• Comparative Genome Viewer (CGV) Tutorials

  • CGV video tutorial: Learn how to use CGV to view assembly-assembly alignments including cross-species alignments with this video tutorial.
  • CGV written tutorial: Get step-by-step instructions on how to use CGV with this tutorial walking you through several case studies.

• NCBI Datasets Tutorials

  • Find a representative protein : 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.
  • Rename downloaded files: 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.
  • Retrieve orthology data : Learn to retrieve ortholog data and metadata using the NCBI Datasets command line tool in this in-depth tutorial.
  • Work with JSON Lines data reports : 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.
  • Access NCBI Genome data in Galaxy : View our quick video guide on how to use NCBI Datasets in Galaxy to access genomic data.

• NCBI Datasets Command Line Tools How-to Guides

  • Retrieve gene data : Find example commands to get gene metadata, download a gene data package, and download an ortholog data package.
  • Retrieve data related to genomes: Learn how to retrieve genomic, transcript and protein sequence, annotation and metadata for assembled genomes.
  • Retrieve data for viruses : View our guide on how to access virus genome sequence and metadata, including a protein data package for SARS-CoV-2.

Workshops

Watch these in-depth videos to learn how to incorporate resources from the NCBI Toolkit into your comparative genomics research.

• Exploring the Relationship Between Two Eukaryotic Genomes Using the Comparative Genome Viewer: Watch this video to learn to how compare two genomes, explore synteny, search for genes, and view pairwise alignment at the sequence level.

• An Introduction to Molecular Evolutionary Analysis with NCBI Datasets and Python: 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.

• Using NCBI Foreign Contamination Screen (FCS) to Remove Contaminants from Genome Assemblies: 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.

CGR Publications

Read all about the NIH Comparative Genomics Resource (CGR) including data and tools in the NCBI Toolkit in these free, publicly available articles

• The NIH Comparative Genomics Resource: addressing the promises and challenges of comparative genomics on human health
• Rapid and sensitive detection of genome contamination at scale with FCS-GX
• The NCBI Comparative Genome Viewer (CGV) is an interactive visualization tool for the analysis of whole-genome eukaryotic alignments
• Exploring and retrieving sequence and metadata for species across the tree of life with NCBI Datasets