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NCBI Resources

Information about determining the best databases to use to answer questions and reviews of commonly used databases.

Basic Local Alignment Search Tool (BLAST)

BLAST homepage

BLAST finds region of similarity between biological sequences.  The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.  It can be run on the web or as a standalone desktop application.  There are specialized BLAST searches for query comparisons such as GEO to look for matches to gene expression profiles OR CD-search to find conserved domains in your sequence.  BLAST is a software, not a database in the traditional sense, but it does perform sophisticated searches like you do in other databases.

BLAST is a registered trademark of NCBI and you must cite it if used in publication

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., "Basic local alignment search tool". Journal of Molecular Biology. 215(3): 403-410 (1990).

Why would I use BLAST?

Finding a statistically significant match based on sequence similarity allows for researchers to:

  • assign functions to unknown sequences
  • compare two or more sequences to each other
  • locate 3D structure records for a given sequence
  • locate similar sequences that bind drugs, organic substances, ions, or nucleic acids
  • identify the portion of a sequence which would best support cloning through the use of the polymerase chain reaction
  • clean suspected cloning vector sequences from cloned sequences

(From Lecture Notes, Librarians Guide to NCBI, Librarians guide to BLAST)

Terms and Definitions

Query: unknown sequence

Subject: known sequence from database

Identity: the degree to which sequences are exactly the same

Similarity: the degree to which two or more sequences resemble each other; can imply similar functions with caveats

Homology: sequence similarity from a common ancestor