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Basic Local Alignment Search Tool (BLAST), available through the National Institute of Health's NCBI network, is a free online search system on the NCBI platform and algorithm for searching genetic data. The BLAST homepage on the NCBI network gives a brief description of how the tool functions:[1]

The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.


The BLAST homepage on NCBI allows users to select from a list of specific species genomes to search, or users can view a list of all genomic BLAST databases. A description of all databases searchable with BLAST can be found in the Blast Program Selection Guide.

The homepage lists a variety of basic BLAST programs that can be run:[1]

  • nucleotide blast - Search a nucleotide database using a nucleotide query. (Algorithms: blastn, megablast, discontiguous megablast)
  • protein blast - Search protein database using a protein query. (Algorithms: blastp, psi-blast, phi-blast)
  • blastx - Search protein database using a translated nucleotide query.
  • tblastn - Search translated nucleotide database using a protein query.
  • tblastx - Search translated nucleotide database using a translated nucleotide query.

The homepage also lists a variety of specialized BLAST searches and databases. The BLAST Program Selection Guide describes all programs/search options available through the system.

Additional Resources

Searchers can find a variety of useful help guides on searching with BLAST through the NCBI Bookshelf. A detailed description of how to correctly search on the NCBI platform using BLAST can be found on Chapter 16 of the NCBI Handbook. A more detailed manual, BLAST® Help, is also available to view online through the NCBI Bookshelf. This manual "documents the BLAST (Basic Local Alignment Search Tool) command line applications developed at the National Center for Biotechnology Information (NCBI)."[2]

The BLAST homepage on NCBI also links a wide variety of help resources (including the previously mentioned guides) through the BLAST help section.

Other Ways to Search with NCBI BLAST

NCBI BLAST is also available through the Patent Lens search system.


  1. 1.0 1.1 "BLAST ®." NCBI BLAST website, Accessed September 7, 2011.
  2. "BLAST® Help." NCBI Bookshelf website, Accessed September 7, 2011.

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