Basic Local Alignment Search Tool – find regions of similarity between biological sequences

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.

BLAST is one of the most widely used bioinformatics programs for sequence searching.

BLAST is a registered trademark of the National Library of Medicine.

There are many different flavors of BLAST searches:

  • The megaBLAST nucleotide-nucleotide search, optimized for very similar sequences (in the same or in closely related species), first looks for an exact match of 28 bases, and then attempts to extend that initial match into a full alignment.
  • The BLASTN nucleotide-nucleotide search looks for more distant sequences.
  • BLASTP performs protein-protein sequence comparison, and its algorithm is the basis of many other types of BLAST searches such as BLASTX and TBLASTN.
  • BLASTX searches a nucleotide query against a protein database, translating the query on the fly.
  • TBLASTN searches a protein query against a nucleotide database, translating the database on the fly.
  • PSI-BLAST first performs a BLASTP search to collect information that it then uses to produce a Position-Specific-Scoring-Matrix (PSSM). A PSSM for a query of length N is an N x 20 matrix. Each of the N columns corresponds to a letter in the query, and each column contains 20 rows. Each row corresponds to a specific residue and describes the probability of related sequences having that residue at that position. PSI-BLAST can then search a database of protein sequences with this PSSM.
  • RPSBLAST (Reverse-Position-Specific BLAST) can very quickly search a protein query against a database of PSSMs that were usually produced by PSI-BLAST.
  • DELTA-BLAST produces a PSSM with a fast RPSBLAST search of the query, followed by searching this PSSM against a database of protein sequences.

Support: Handbook, FAQ
Developer: Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, NCBI
License: Public domain

BLAST is written in C and C++. Learn C with our recommended free books and free tutorials. Learn C++ with our recommended free books and free tutorials.

Return to Bioinformatics Tools Home Page

Ongoing series
Linux for StartersNew to Linux? Read our Linux for Starters series.
Free and Open Source SoftwareThe largest compilation of the best free and open source software in the universe. Supplied with our legendary ratings charts.
Linux ReviewsHundreds of in-depth reviews offering our unbiased and expert opinion on software.
Alternatives to GoogleAlternatives to Google's Products and Services examines your options to migrate from the Google ecosystem with open source Linux alternatives.
MicrosoftAlternatives to Microsoft's Products and Services recommends open source Linux software.
Linux System ToolsEssential Linux system tools looks at small, indispensable utilities, useful for system administrators as well as regular users.
Linux ProductivityLinux utilities to maximise your productivity. Small, indispensable tools, useful for anyone running a Linux machine.
Home Computer EmulatorsHome computers became commonplace in the 1980s. Emulate home computers including the Commodore 64, Amiga, Atari ST, ZX81, Amstrad CPC, and ZX Spectrum.
Now and ThenNow and Then examines how promising open source software fared over the years.
Linux at HomeLinux at Home looks at a range of home activities where Linux can play its part, making the most of our time at home, keeping active and engaged.
Linux CandyLinux Candy opens up to the lighter side of Linux. Have some fun!
Best Free Android AppsBest Free Android Apps. There's a strict eligibility criteria for inclusion in this series
Programming BooksThese best free books accelerate your learning of every programming language
Programming TutorialsThese free tutorials offer the perfect tonic to the free programming books series
Stars and StripesStars and Stripes is an occasional series looking at the impact of Linux in the USA
Share this article

Share your Thoughts

This site uses Akismet to reduce spam. Learn how your comment data is processed.