How BLAST Works and Using Web BLAST Effectively


The NCBI workshop is designed for beginning BLAST users or people wanting a refresher on how blast works and some tips on how to run effective BLAST searches.

– Materials: 2022-10_Basic-Web-BLAST
– Slides, PDF: workshop_BLAST_Oct2022.pdf
– Recording: has been added (See Workshop Video Tab on Materials page.)

This workshop is suitable both for beginner Web BLAST users and those who would like an update and some tips and tricks to enhance their ability to use this powerful bioinformatics tool. The topics we cover in this hands-on Web BLAST workshop come directly from feedback and questions we’ve received from people like you. In this workshop, you’ll learn how to:
  • Adjust search settings to avoid errors and reduce search times
  • Choose the best database
  • Try out the new clustered nr database
  • Customize and download the search results
  • Display your BLAST results in an interactive sequence viewer

Blast output example

BLAST: Basic Local Alignment Search Tool

BLAST is one of the most widely used bioinformatics tools in the world, most often on the NCBI web site.

BLAST was originally designed to use a nucleotide or protein sequence to search and quickly find similar sequences. BLAST is now often used for identification of: the gene name and/or source organism of the sequence, related sequences from other organisms (homologs), as well as the location of a sequence within a larger reference sequence, such as a chromosome or genome.


Basic Local Alignment Search Tool (BLAST) (Lobo, I. (2008) Basic Local Alignment Search Tool (BLAST). Nature Education 1(1):215)


Altschul, S. F., et al. Basic Local Alignment Search Tool. Journal of Molecular Biology 215, 403–410 (1990) doi:10.1016/S0022-2836(05)80360-2 (pubmed: 2231712)

Altschul, S. F., et al. Issues in searching molecular sequence databases. Nature Genetics 6, 119–129 (1994) doi:10.1038/ng0294-119 (link to article)