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

Popular series
Free and Open Source SoftwareThe largest compilation of the best free and open source software in the universe. Each article is supplied with a legendary ratings chart helping you to make informed decisions.
ReviewsHundreds of in-depth reviews offering our unbiased and expert opinion on software. We offer helpful and impartial information.
Alternatives to Proprietary SoftwareReplace proprietary software with open source alternatives: Google, Microsoft, Apple, Adobe, IBM, Autodesk, Oracle, Atlassian, Corel, Cisco, Intuit, and SAS.
GamesAwesome Free Linux Games Tools showcases a series of tools that making gaming on Linux a more pleasurable experience. This is a new series.
Artificial intelligence iconMachine Learning explores practical applications of machine learning and deep learning from a Linux perspective. We've written reviews of more than 40 self-hosted apps. All are free and open source.
Guide to LinuxNew to Linux? Read our Linux for Starters series. We start right at the basics and teach you everything you need to know to get started with Linux.
Alternatives to popular CLI tools showcases essential tools that are modern replacements for core Linux utilities.
System ToolsEssential Linux system tools focuses on small, indispensable utilities, useful for system administrators as well as regular users.
ProductivityLinux utilities to maximise your productivity. Small, indispensable tools, useful for anyone running a Linux machine.
AudioSurveys popular streaming services from a Linux perspective: Amazon Music Unlimited, Myuzi, Spotify, Deezer, Tidal.
Saving Money with LinuxSaving Money with Linux looks at how you can reduce your energy bills running Linux.
Home ComputersHome 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. It can be a bumpy ride.
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 reveals the lighter side of Linux. Have some fun and escape from the daily drudgery.
DockerGetting Started with Docker helps you master Docker, a set of platform as a service products that delivers software in packages called containers.
Android AppsBest Free Android Apps. We showcase free Android apps that are definitely worth downloading. There's a strict eligibility criteria for inclusion in this series.
Programming BooksThese best free books accelerate your learning of every programming language. Learn a new language today!
Programming TutorialsThese free tutorials offer the perfect tonic to our free programming books series.
Linux Around The WorldLinux Around The World showcases usergroups that are relevant to Linux enthusiasts. Great ways to meet up with fellow enthusiasts.
Stars and StripesStars and Stripes is an occasional series looking at the impact of Linux in the USA.
Notify of

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

Inline Feedbacks
View all comments