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Tips to use of NCBI BLAST and other NCBI tools

The National Center for Biotechnology Information (NCBI) provides one of the most extensive sets of web-based tools for biological research. These tools are indispensable when planning genomics experiments, including for qPCR, NGS, and CRISPR.

In this presentation, Dr Matt McNeill takes a practical look at getting started with the wealth of NCBI tools, and shares some relevant tips to help you sift through the tools and options that we regularly use.

In particular, he focuses on commonly adjusted parameters that will allow you to more effectively use the powerful NCBI Basic Local Alignment Algorithm Tool (BLAST) to identify off-target hybridization/annealing events. Dr McNeill also covers practical examples using NCBI tools to design assays.

Covered in this video:
What is NCBI? (National Center for Biotechnology Information)

NCBI's available tools
User Story: Previously published paper
User Story: We want to follow up on this work; 
User Story:Getting your Gene Sequences
User Story: Gene list
User Story: Identify your gene list
    - Translating IDs
    -  Genome Build
    -  Downloading Fasta Sequences
    -  Log File Page

    -  Downloading Output
    -  FASTA File format
User Story: Checking for off-target CRISPR events
    -  Using NCBI BLAST
    -  Using BLASTN
User Story: Checking off-target qPCR primers (PCR)
User Story: Checking off-target qPCR primers (Primer Blast)

Summary:
Gene Lookup--Gene Database; Gene Symbol Translation-bioDB; Fasta Sequence Download--Gene database, Batch entrez; Single Sequence Uniqueness--BLASTN; Primer Uniqueness--Primer BLAST


Related Decoded Articles:

How to Use NCBI Blast to Locate Primers

Published on: August 24, 2016