What Is BLAST and Which BLAST Search Should You Use?

Updated

BLAST (Basic Local Alignment Search Tool) finds regions of local similarity between biological sequences. It compares a nucleotide or protein query against sequence databases and calculates the statistical significance of matches, which lets you infer functional and evolutionary relationships between sequences and identify members of gene families. Use the standard Web BLAST when you have one sequence and want to know what it resembles; switch to a specialized search when your goal is narrower, such as designing primers, comparing two sequences end to end, or locating conserved domains.

What BLAST actually does

BLAST does not align two sequences from start to finish. It looks for local regions of similarity — short stretches where your query and a database sequence match well — and then scores those regions.

Two outputs matter most when you read a result:

  • Alignment score — how well a local region matches; higher means a better match under the scoring scheme used.
  • E-value — the expected number of matches this good that would occur by chance in a database of that size. Smaller is stronger.

Because matches are local, a single query can produce several separate hits, and a hit can cover only part of your sequence. That is a feature, not an error: it is how BLAST detects shared domains between otherwise different proteins.

Choosing the right search

The BLAST site groups its tools by purpose. Match the tool to your goal:

Your goal Tool What it does
General "what is this sequence?" Web BLAST Compares nucleotide or protein queries to sequence databases
Search across many genomes BLAST Genomes Enter an organism common name, scientific name, or tax ID (e.g., Human, Mouse, Rat, Microbes)
Quick protein identification SmartBLAST Finds proteins highly similar to your query
Design PCR primers Primer-BLAST Designs primers specific to your PCR template
Compare two sequences across their full length Global Align Needleman-Wunsch alignment over the entire span
Find conserved domains CD-search Finds conserved domains in your sequence
Find similar domain architecture CDART Finds sequences with similar conserved domain architecture
Search immune sequences IgBLAST Searches immunoglobulins and T cell receptor sequences
Check for vector contamination VecScreen Searches sequences for vector contamination
Align multiple sequences Multiple Alignment Aligns sequences using domain and protein constraints

If you are unsure, start with Web BLAST. The specialized tools exist because the general search answers a different question — Primer-BLAST, for example, is built around primer specificity to a template, not around finding the closest relative of a sequence.

Running BLAST beyond the website

The web interface is one of several ways to run BLAST. The site also offers:

  • Download BLAST — get BLAST databases and executables to run locally.
  • Use BLAST API — call BLAST from your own application.
  • Use BLAST in the cloud — start an instance at a cloud provider.

The choice is about scale and automation: interactive one-off queries fit the web interface, while repeated or programmatic searches fit the API, local executables, or a cloud instance. Local and cloud options also matter when you need to search custom databases or control where your data lives.

Reading results without over-reading them

A strong hit is evidence, not proof. Before treating a match as definitive:

  • Check coverage — does the alignment span most of your query, or just a fragment?
  • Check the E-value in context of the database size, not as an absolute pass/fail.
  • Expect multiple hits for multi-domain proteins; each may reflect a different shared region.
  • Treat functional or evolutionary inference as a hypothesis to confirm by other means.

The practical rule: use BLAST to generate candidates and relationships, then verify the ones that matter.