BLAST — Basic Local Alignment Search
VigyanLLM is an autonomous BLAST sequence alignment tool that performs local alignment using the BLAST algorithm. Unlike standard web BLAST tools, it runs entirely on your local infrastructure with BLASTN, BLASTP, and BLASTX searches against private reference databases — ensuring zero sequence data leaves your institution.
| Input | Output |
|---|---|
| Nucleotide query (FASTA) | BLASTN alignments against nucleotide database with E-values, bit scores |
| Protein query (FASTA) | BLASTP alignments against protein database with E-values, bit scores |
| Translated nucleotide query (FASTA) | BLASTX alignments against protein database |
| Protein query + Translated nucleotide DB (FASTA) | tBLASTN alignments against translated nucleotide database |
Query
Actions
Results
Frequently Asked Questions About BLAST
Everything you need to know about BLAST sequence alignment
What is BLAST?
BLAST (Basic Local Alignment Search Tool) is a bioinformatics algorithm that finds regions of similarity between biological sequences — DNA, RNA, or protein. It compares a query sequence against a database of known sequences and identifies the most similar matches. BLAST is one of the most widely used tools in molecular biology, genomics, and computational biology.
Why is BLAST used?
BLAST is used to identify unknown sequences, find homologous genes across species, check primer specificity, annotate genomes, discover conserved domains, and detect evolutionary relationships. It helps researchers determine what a newly sequenced DNA fragment might be by finding its closest known relatives in public databases.
How does the BLAST algorithm work?
BLAST works by breaking the query sequence into short overlapping "words" (typically 3 residues for protein, 11 bases for DNA). It first finds exact matches to these words in the database (seeding), then extends those matches in both directions to build longer alignments. Finally it computes statistical significance using E-values and bit scores to rank the results.
What do E-value and bit score mean?
The E-value (Expect value) indicates the number of alignments with a similar score that would be expected to occur by random chance in the database. Lower E-values indicate more significant matches. An E-value of 0.0 means the match is highly significant. The bit score is a normalized score that is independent of database size, making it useful for comparing results across different searches. Higher bit scores indicate better alignments.
How is BLAST used in primer design?
BLAST is critical for primer specificity checking. Before ordering primers, researchers BLAST the primer sequences against the target genome and closely related genomes to ensure the primers will amplify only the intended target region. High identity to off-target regions indicates potential non-specific amplification. VigyanLLM integrates BLAST directly into its primer design workflow for automated specificity validation.
What databases does BLAST search?
Common BLAST databases include NCBI nt (non-redundant nucleotide database covering GenBank, EMBL, DDBJ), RefSeq RNA (curated RNA sequences), and NCBI nr (non-redundant protein database). VigyanLLM supports all three and allows organism-specific filtering to narrow results to relevant species.
What is the difference between BLASTn and BLASTp?
BLASTn compares a nucleotide query against a nucleotide database (DNA vs DNA). BLASTp compares a protein query against a protein database (amino acid vs amino acid). Protein comparisons can detect more distant evolutionary relationships because the genetic code is degenerate — the same protein can be encoded by many different DNA sequences. VigyanLLM supports both nucleotide and protein BLAST searches.
How do I interpret BLAST results?
BLAST results show several key metrics: Identity % tells you how similar the query and subject sequences are. Alignment length shows how much of the sequence matched. E-value indicates statistical significance. A good BLAST hit typically has high identity (>90%), high query coverage (>80%), and a very low E-value (close to 0.0). Always check the subject description and species to confirm the match is biologically meaningful.
Is BLAST free to use?
Yes. BLAST is freely available through NCBI and through VigyanLLM. VigyanLLM provides free BLAST searches with no login required, integrated directly with primer design, MSA, and other bioinformatics tools on the platform.