Genomics · Database
NCBI BLAST
NCBI BLAST finds regions of local similarity between biological sequences to infer functional and evolutionary links.
What NCBI BLAST is
The Basic Local Alignment Search Tool (NCBI BLAST) compares query nucleotide or protein sequences against sequence databases. It identifies regions of local sequence similarity and calculates the statistical significance of those matches.
Biologists and computational researchers use the system to infer functional and evolutionary relationships between sequences and to identify members of gene families. Searches run against primary sequence collections including core_nt, nr, SwissProt, RefSeq, and ClusteredNR.
How it is organised
BLAST matches nucleotide or amino acid queries against sequence repositories to find regions of local alignment, evaluating each alignment using statistical significance calculations. In addition to direct nucleotide-to-nucleotide and protein-to-protein comparisons, it can translate sequences across different reading frames via methods such as blastx (translated nucleotide queries against protein databases) and tblastn (protein queries against translated nucleotide databases), or perform whole-span pairwise comparisons using the Needleman-Wunsch global alignment algorithm.
The system also incorporates domain- and application-specific processing workflows. These include conserved domain searches (CD-search and CDART) that detect structural and functional motifs, multiple sequence alignment using domain constraints, automated PCR primer design, and targeted sequence profiling for specific loci or vector artefacts.
Key facts
- Input formats
- Nucleotide and protein sequences
- Reference databases
- core_nt, nr, SwissProt, RefSeq, ClusteredNR
- Alignment algorithms
- Local alignment, Needleman-Wunsch global alignment
- Access methods
- Web BLAST, Standalone executables, API, Cloud instances
What you can use it for
- Gene family and homology identification
- Comparing novel nucleotide or protein queries against the nr, core_nt, or RefSeq databases to deduce function and identify related gene family members.
- PCR primer design
- Designing oligonucleotide primers that are specific to a designated polymerase chain reaction (PCR) template using Primer-BLAST.
- Conserved domain analysis
- Locating conserved domains or matching domain architectures in protein sequences using CD-search and CDART.
- Vector contamination screening
- Screening newly generated sequence data for artificial vector contamination using VecScreen.
- Immune receptor profiling
- Searching and analysing immunoglobulin and T-cell receptor sequences via IgBLAST.
Query it here
The research agent queries NCBI BLAST directly — no account, no API key — and every answer links back to the record it came from. Ask in plain language and it writes the query.
Strengths and limits
Good at
- Calculates the statistical significance of alignments to help distinguish meaningful biological matches from chance similarities.
- Supports cross-modality searches, including translated nucleotide-to-protein and protein-to-translated-nucleotide matching.
- Offers specialised modules tailored for primer design, vector screening, conserved domain mapping, and immune receptor analyses.
Questions
Can I search NCBI BLAST without writing code?
Yes. The research agent queries NCBI BLAST directly, with no account or API key, and cites the record behind every answer. Ask in plain language — for a gene, a protein, a compound or a study — and it builds the query for you.
Can I reuse data from NCBI BLAST?
NCBI BLAST publishes its own terms of use; read them on https://blast.ncbi.nlm.nih.gov before reusing its records.
Which sequence databases does NCBI BLAST query?
NCBI BLAST queries databases including core_nt, nr, SwissProt, RefSeq, and ClusteredNR, in addition to dedicated organism genomes such as human, mouse, rat, and microbes.
How can BLAST be integrated into computational pipelines?
BLAST can be executed programmatically via the BLAST API, run locally using downloadable standalone executables and databases, or deployed through cloud provider instances.
What is the difference between standard BLAST and the Global Align tool?
Standard BLAST identifies regions of local similarity between sequences, whereas the Global Align tool compares two sequences across their entire span using the Needleman-Wunsch algorithm.
What does SmartBLAST do?
SmartBLAST is a specialised search tool designed to find proteins that are highly similar to a user query sequence.
Written from NCBI BLAST's own website and reference material. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.