DIMACS Short Course: A Field Guide to GenBank and NCBI Molecular Biology Resources

March 1 - 2, 2005
DIMACS Center, CoRE Building, Rutgers University

Organizers:

Tamar Barkay, Department of Biochemistry and Microbiology, barkay@AESOP.Rutgers.edu

Paul Ehrlich, BIOMAPS Institute, pehrlich@lutece.rutgers.edu

Mel Janowitz, DIMACS, melj@dimacs.rutgers.edu

Tara Matise, Department of Genetics, matise@biology.rutgers.edu

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. Further information about NCBI may be found at http://www.ncbi.nlm.nih.gov

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

Topics covered will include:

• 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 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 LocusLink
    • UniGene
    • Variation Data (SNPs)
    • The Human, Mouse and Rat Genomes
    • The Map Viewer
    • Other Genomes

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