NCBI Functional Genomics Workshop

• 9am to 12pm – An Update on NCBI BLAST and Other Sequence Analysis Tools
  • This workshop highlights new displays and features and introduces best practices for use of NCBI BLAST services. You will learn when and how to use important but often misunderstood aspects of the BLAST programs, specialized services, and databases. You will explore other important sequence analysis services, including Primer BLAST, an oligonucleotide primer designer and specificity checker, and COBALT, a multiple protein sequence alignment tool. Finally, you will see brief demonstrations of standalone BLAST and related tools, including SRA-Toolkit BLAST and Magic-BLAST.Specifically, you will learn to:
    • Select the correct NCBI alignment tool for your task
    • Choose the best BLAST database for your search goal
    • Understand and use the new BLAST results page, output formats and statistics
    • Display BLAST results in genomic context using graphical displays
    • Analyze nucleotide primers: design, check the specificity, and display primer alignments
    • Assess the taxonomic distribution of your BLAST matches and use the TreeViewer display to visualize relationships
    • Use standalone BLAST, Magic-BLAST and SRA-BLAST to search local databases and remote database on the NCBI server
• 1pm to 4pm – NCBI Resources for Animal and Plant Genomics Research
  • This workshop focuses on NCBI’s web-based resources for accessing and analyzing genome assemblies and annotation data, with an emphasis on non-human organisms. You will learn which databases at NCBI best meet your needs, including Genome, Assembly, BioProject, Taxonomy, Gene, and SRA. We will also briefly discuss NCBI’s analysis and stand-alone tools, such as the Genome Data Viewer (GDV), SRA Toolkit and Magic-BLAST.In this workshop you will learn how to:
    • Find, view and download the latest genome assembly data
    • Access and download annotation data for genes, transcripts and proteins
    • Find gene-specific information, including genomic context, orthologs and literature
    • Use GDV to visualize both NCBI and external data (Track Hubs or your own data).

April 16, 2020

• 9am to 12pm – NCBI Resources for Pathogen (Bacteria & Virus) Genomics Research
  • In this workshop, you will learn to use NCBI resources to search, access, and analyze animal and plant pathogen (bacteria and virus) data from individual isolates and metagenomes.  You will explore some general resources for all organisms, as well as some newly developed resources for bacteria and viruses. In addition, you will briefly see how to access and analyze data using standalone tools, such as the SRA Toolkit and Magic-BLAST.Specifically, you will learn to:
    • Find, browse, and download genome-, gene-, protein- and sequence read-level data for individual bacterial and viral pathogens and metagenomes
    • Access and display precomputed genome analyses and perform your own analyses of assembled and unassembled genomic data to identify organisms and genes
    • Find sequences, variants, antibiotic resistance genes using BLAST services, including SRA-BLAST
    • Explore the new and developing NCBI Virus and Pathogen Detection Project resources.
• 1pm to 4pm – NCBI Resources for Gene Expression and Genetic Variation Research
  • This workshop focuses on NCBI’s web-based resources for accessing gene expression and genetic variation data for non-human organisms. You will learn about NCBI’s gene expression databases, including Gene, GEO, and SRA. You will learn how you can leverage SRA data for your gene expression and genetic variation analyses. We will also briefly discuss NCBI’s analysis and stand-alone tools, such as GEO2R, the Genome Data Viewer (GDV), SRA Toolkit and Magic-BLAST.In this workshop you will learn how to:
    • Find gene-specific expression data in Gene and GEO databases
    • Find and explore experimental study information in the GEO database
    • Access and analyze SRA data
    • Use GDV as a variant analysis tool

Peter Cooper, Ph.D. is an NCBI Customer Experience team member and Team Lead for Strategic Communications (Education, Social Media, Conferences). For the past 22 years, he has provided user support for the NCBI molecular databases and tools and has directed scientific education and outreach efforts including popular courses and workshops such as the long‐running NCBI Field Guide, Discovery Workshops and Modular Workshops and numerous short courses at Cold Spring Harbor Laboratories, the Jackson Laboratory and Woods Hole Oceanographic Institution. He has research experience in biochemistry and marine biology.

Wayne Matten, Ph.D. is an NCBI Customer Experience team member. Since 2000, he has provided user support including teaching courses and workshops on a wide range of NCBI resources. Wayne is part of the BLAST-help group, maintains the NCBINLM YouTube channel, and creates tutorial videos on NCBI tools and resources. His research background is in biochemistry/molecular biology focused on signal transduction mechanisms involving oncogenes.