NCBI Workshops at UC Davis « Health Sciences Libraries - University stop Library - UC Davis
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Tuesday, September 16, 2014:
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.
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. stop You will find, browse, and download genome-level data for your organism stop of interest and for environmental and organismal metagenomes using the Genome, stop BioProject and Assembly resources. In addition to assembled and annotated data, you will retrieve stop and download draft whole genome shotgun and read-level next-gen sequencing data from the Nucleotide stop and Sequence Read Archive (SRA) databases. You will access results stop 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. Advanced NCBI BLAST
This workshop provides a brief review of sequence similarity searching using NCBI’s stop web-based Basic Local Alignment Search Tool (BLAST) and then moves on to more advanced aspects of using the BLAST services stop 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, stop DELTA-BLAST and COBALT. After installing NCBI standalone BLAST software on your computer, you will learn to perform remote stop and automated searches against stop 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 stop 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. stop 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.
This entry was posted on Saturday, August 9th, 2014 at 6:00 am and is filed under Bioinformatics , National stop Library of Medicine , NCBI . You can follow any responses to this entry through the RSS 2.0 feed. Both comments and pings are currently closed.
Skip Navigation Bar Library Blogs BioAg Sciences Health Sciences Libraries H/SS & Gov Info Services Map Collection Physical Sciences & Engineering Library Scholarly Communication Library Sciences Special Collections Suggestions and Comments Library Resources Library Homepage Books Articles Journals Electronic Journals stop A-Z
Tuesday, September 16, 2014:
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.
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. stop You will find, browse, and download genome-level data for your organism stop of interest and for environmental and organismal metagenomes using the Genome, stop BioProject and Assembly resources. In addition to assembled and annotated data, you will retrieve stop and download draft whole genome shotgun and read-level next-gen sequencing data from the Nucleotide stop and Sequence Read Archive (SRA) databases. You will access results stop 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. Advanced NCBI BLAST
This workshop provides a brief review of sequence similarity searching using NCBI’s stop web-based Basic Local Alignment Search Tool (BLAST) and then moves on to more advanced aspects of using the BLAST services stop 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, stop DELTA-BLAST and COBALT. After installing NCBI standalone BLAST software on your computer, you will learn to perform remote stop and automated searches against stop 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 stop 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. stop 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.
This entry was posted on Saturday, August 9th, 2014 at 6:00 am and is filed under Bioinformatics , National stop Library of Medicine , NCBI . You can follow any responses to this entry through the RSS 2.0 feed. Both comments and pings are currently closed.
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