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NCBI Workshops at UC Davis

NCBI 2014 cropped

September 15 – 16, 2014

Presented by Peter Cooper, PhD & Wayne Matten, PhD
National Center for Biotechnology Information (NCBI)

2205 Haring Hall

Pre-registration is complete. 

You are welcome to register on-site, 15 minutes prior to the start of each workshop.

This series of in-person workshops will focus on the following:

Monday, September 15, 2014:

9-11:30am             Navigating NCBI Molecular Data Using the Integrated Entrez System and BLAST

1-3:30pm               NCBI Genomes, Assemblies and Annotation Products: Microbes to Human

Tuesday, September 16, 2014:

9am-11:30am       Advanced NCBI BLAST

1-3:30pm               Gene Expression Resources at NCBI

Workshop format will include lecture and hands-on activities.  Participants are encouraged to bring laptops for practice sessions.  Workshops are free of charge and open to UC Davis faculty, students and staff, as well as others in the Sacramento region.  Guest wireless Internet access will be provided.

Printed handouts will NOT be provided.  Link to course materials:

Questions?       Contact


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For a detailed description of workshops: 

NCBI Workshops at UC Davis – September 2014

Detailed Course Descriptions

Navigating NCBI Molecular Data Using the Integrated Entrez System and BLAST

This workshop provides an introduction to the NCBI molecular databases and how to access the data using the Entrez text-based search system and BLAST sequence similarity search tool. You will learn the varied types of available molecular data, and how to find and display sequence, variation, genome information using a single gene as an example to navigate across the integrated databases (Gene, Nucleotide, Protein, dbSNP and other resources).

NCBI Genomes, Assemblies and Annotation Products: Microbes to Human

You will learn how NCBI processes genome-level data and produces annotation through the prokaryotic and eukaryotic genome annotation pipelines.  You will find, browse, and download genome-level data for your organism of interest and for environmental and organismal metagenomes using the Genome, BioProject and Assembly resources. In addition to assembled and annotated data, you will retrieve and download draft whole genome shotgun and read-level next-gen sequencing data from the Nucleotide and Sequence Read Archive (SRA) databases. You will access results of precomputed analyses of genomes, as well as perform your own analyses of assembled and unassembled genomic data using NCBI’s genome BLAST and SRA-BLAST services.


This workshop provides a brief review of sequence similarity searching using NCBI’s web-based Basic Local Alignment Search Tool (BLAST) and then moves on to more advanced aspects of using the BLAST services and software. You will learn how to optimize basic web BLAST searches, how to use the advanced protein similarity searches and alignment tools PSI-BLAST, DELTA-BLAST and COBALT. After installing NCBI standalone BLAST software on your computer, you will learn to perform remote and automated searches against the NCBI BLAST databases using standalone BLAST’s remote option. You will also learn to use BLAST’s URL-API as well as VDB BLAST to remotely search next-gen data at the Sequence Read Archive.  Finally, you will learn about the new cloud-based BLAST service as an option for high volume searches.

Gene Expression Resources at NCBI

You will find, display and analyze microarray and sequence-based expression data that are stored in the Gene Expression Omnibus (GEO), Sequence Read Archive (SRA), UniGene, and Epigenomics databases to investigate the potential for expression of transcript splice variants and examine the levels of expression under varied experimental conditions as well as in different tissues and disease states. You will analyze Microarray data the on-demand GEO2R tool and will explore the precomputed transcript analyses that are displayed on the UniGene and GEO Profiles pages. You will explore genome-aligned RNA-Seq data through the Gene database’s sequence viewer displays and analyze raw RNA-Seq reads in the SRA database using NCBI’s SRA-BLAST service. Finally, you will browse DNA and chromatin modification data relevant to gene expression using the Epigenomics browser.



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