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Field Guide to GenBank and NCBI Molecular Biology Resources
January 27-28, 2005

 

Intended Audience:

The course is designed for principal investigators, postdoctoral fellows, graduate and advanced undergraduate students and others who work with biological sequence data. Both experienced and novice users of NCBI's tools and resources will benefit.

ATTENTION: The course is limited to members of the Notre Dame community due to budget constraints.

Registration:

All hands-on sessions are full/closed. The lecture is still open. Please register for the lecture.

The course is free but REGISTRATION IS REQUIRED.

Workshop sessions are optional.  Lecture attendance is a mandatory prerequisite for any workshop session.

Course Description:

The National Center for Biotechnology Information (NCBI) presents A Field Guide to GenBank and NCBI Molecular Biology Resources, a lecture and hands-on computer workshop on GenBank and related databases covering effective use of the Entrez databases and search service, the BLAST similarity search engine, genome data and related resources.

Now featuring the NCBI assembly and annotation of human, mouse and rat genomes, the updated map viewer genome displays, the new genome-specific BLAST pages, the new NCBI curated conserved domains, and Cn3D 4.1.

The course has two parts: a 3-hour morning lecture followed by optional 2-hour instructor led computer workshops in the afternoon. Additional workshops are available on the following day. Due to the limited number of workstations, multiple workshops will be offered on two dates in order to accommodate as many people as possible. The same content is covered in each workshop.

Note: Workshop sessions are limited to 23 people per session and we expect them to fill up quickly.

Topics:

  • GenBank Database: description and scope
  • The NCBI Derivative Databases: RefSeqs
  • Database Searching using Entrez
    • Neighboring and Links
    • Entrez searching
  • The NCBI Structures Database
    • The Molecular Modeling Database (MMDB)
    • Structural Alignments
    • Viewing Structures and Structural Alignments with Cn3D
  • Similarity Searching using NCBI BLAST
    • Local Alignment Statistics
    • Scoring Systems
    • Using BLAST 2.2.8 web services
    • PSI-BLAST
    • RPS-BLAST (CDD Search)
    • Specialized BLAST pages
  • Genomic Resources at NCBI
    • Complete Microbial Genomes in Entrez
    • Higher Genome Resources
      • RefSeq and Genes
      • UniGene
      • Variation Data (SNPs)
      • The Human, Mouse and Rat genomes
      • The Map Viewer
      • Other Genomes


    Instructor: Steve Pechous

    Lecture:

    Place: McKenna Hall Auditorium
    Date:  Thursday, January 27, 2005
    Size:   200 participants
    Time:  0830 - 1130

    Workshops:

    Place:  107 Coleman-Morse
    Date:   Thursday, January 27, 2005
    Size:    23 participants in each session
    Times: 1300 - 1500 Session 1                    
               1530 - 1730 Session 2

    Date:   Friday, January 28, 2005
    Size:    23 participants in each session
    Times: 0800 - 1000 Session 3
               1030 - 1230 Session 4
               1400 - 1600 Session 5
     
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