NCBI Workshop - A Practical Guide to NCBI BLAST

Event
Wednesday, October 5, 2016 - 8:00am
Event Type: 

National Center for Biotechnology Information (NCBI) workshops

  • Drs. Peter Cooper and Wayne Matten of NCBI will conduct the workshops

October 4, 5 and 6
8 - 11:00 a.m.

  • Hands-on Workshop. Seating is limited.

  • Pre-registration is required. RSVP to reserve your seat.

  • Register through Learn@ISU

  • Questions about registration?  Contact: Jody A. Kalvik, jkalvik@iastate.edu, 515-294-6117

October 4
Navigating NCBI Molecular Data
Using the Integrated Entrez System and BLAST

An introduction to the NCBI molecular databases, how to access the data using the Entrez text-based search system and BLAST sequence similarity search tool. Learn about the varied types of available molecular data, and how to find and display sequence, variation, genome information using organism sources (Taxonomy), data sources (Bioproject) and emphasizing the central role of the gene as an organizing concept to navigate across the integrated databases (Gene, Nucleotide, Protein, dbSNP and other resources).

Wed., Oct. 5
A Practical Guide to NCBI BLAST

Highlights features and demonstrates practical aspects of using the NCBI BLAST service. Learn about features including: access from the Entrez sequence databases; the new genome BLAST service quick finder; the integration and expansion of Align-2- Sequences; organism limits and other filters; re-organized databases; formatting options and downloading options; and TreeView displays. Learn about important sequence analysis services associated with BLAST including: Primer BLAST, COBALT; and MOLE-BLAST.

Thurs., Oct. 6
EDirect: Command Line Access to
NCBI’s Biomolecular Databases

Allows easy command line access for searching and retrieving literature (PubMed) and accessing NCBI’s biomolecular (Gene, Nucleotide, sequence databases, etc.) records. Advantages include: direct commandline access to NCBI’s databases without writing Perl or Python scripts, construction of custom pipelines for processing data, built-in batch access, and the ability to generate highly flexible custom output reports.

8 to 9 a.m. Basic introduction to the Unix/Linux command line interface.
9 to 11 a.m. How to use EDirect to set-up simple pipelines to retrieve and process data from PubMed, Gene, and the Nucleotide and Protein sequence databases. Access to EDirect installed in a Linux environment on a cloud service will be provided.

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