Sequence search · Software
BLAST+
Finds regions of local similarity and calculates statistical significance across nucleotide and protein sequences.
What BLAST+ is
BLAST+ (Basic Local Alignment Search Tool) is a sequence alignment suite maintained by the National Center for Biotechnology Information (NCBI). It compares nucleotide or protein query sequences against sequence databases to locate matching regions.
The software evaluates the statistical significance of matches to help researchers identify related biological sequences. These results are used to infer evolutionary and functional relationships and to detect members of gene families.
How it works
BLAST+ aligns nucleotide or protein sequences against database targets by finding regions of local similarity. The tool evaluates the statistical significance of each match to separate biologically meaningful alignments from background matches. In addition to direct nucleotide-to-nucleotide and protein-to-protein searches, it supports translated searches such as blastx and tblastn to match nucleotide sequences against protein databases and vice versa.
The platform also incorporates specialised alignment algorithms and pipelines. These include full-span global pairwise alignments using the Needleman-Wunsch algorithm, conserved domain searches, multiple sequence alignments guided by domain constraints, and specialised search tools for primer design, vector contamination, and immune receptors.
Key facts
- Version
- 2.16.0
- Category
- Sequence search
- Input sequence types
- Nucleotide and protein sequences
- Alignment types
- Local alignment and Needleman-Wunsch global alignment
What you can use it for
- Functional and evolutionary inference
- Comparing novel nucleotide or protein sequences against reference databases to infer their biological functions and evolutionary origins.
- Gene family identification
- Searching sequence databases to identify and characterise homologous members belonging to specific gene families.
- PCR primer design
- Designing template-specific polymerase chain reaction primers using Primer-BLAST.
- Immunoglobulin and T cell receptor profiling
- Searching and matching immunoglobulin and T cell receptor sequences using IgBLAST.
- Vector contamination detection
- Screening sequence data against vector sequence databases using VecScreen to eliminate contamination.
- Conserved domain annotation
- Locating conserved domains and domain architectures in protein sequences using CD-search and CDART.
Run it here
BLAST+ is preinstalled on the machine behind every research conversation. Ask the agent in plain language, or give it the exact command — it runs it, reads the output and explains it.
Try asking
“BLAST these protein sequences against each other and report the best hits.”
Strengths and limits
Good at
- Calculates the statistical significance of identified local sequence matches across nucleotide and protein databases.
- Supports cross-type comparisons through translated nucleotide queries and databases.
- Provides specialised workflows for primer design, vector screening, conserved domain mapping, and immune receptor analysis.
Questions
Can I run BLAST+ online without installing it?
BLAST+ is preinstalled on the machine behind every research conversation. Ask the agent in plain language, or give it the exact command — it runs it, reads the output and explains it.
What licence is BLAST+ under?
BLAST+ is published under its authors' own licence; the project page at https://blast.ncbi.nlm.nih.gov/ states it.
What sequence types can BLAST+ search?
BLAST+ accepts biological sequences composed of either nucleotide or protein sequences.
Does BLAST+ support global sequence alignment?
Yes, it provides a Global Align mode that compares two sequences across their entire length using the Needleman-Wunsch algorithm.
Can translated nucleotide queries be searched against protein databases?
Yes, translated nucleotide workflows such as blastx and tblastn allow searches between translated nucleotide sequences and protein databases.
Written from BLAST+'s own README and project page. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.