Search Parameters
This tool utilizes NCBI BLAST services to search sequence databases. Search times vary based on query length, database size, and server load. Large queries may take several minutes.
This tool utilizes NCBI BLAST services to search sequence databases. Search times vary based on query length, database size, and server load. Large queries may take several minutes.
This tool sends your query to NCBI BLAST and shows alignments and hit statistics when the job completes. Effective sequence length (after FASTA headers are stripped) must be 10–50,000 characters. Match blastn or blastp, your alphabet, and the database you choose.
> header) or raw sequence into Input Sequence (FASTA format), or use Or upload FASTA file (.fasta, .fa, .txt). One query per submission.
Scope: Search runs on NCBI servers; availability and wait times are not controlled by this tool. Only blastn and blastp are exposed here—for blastx, tblastn, or other programs, use NCBI BLAST directly. For research and teaching, not clinical use.
BLAST (Basic Local Alignment Search Tool) is an algorithm for comparing biological sequences. It works by finding regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches, helping identify similar genes or proteins across species.
Choose 'blastn' for nucleotide-to-nucleotide comparisons (DNA/RNA sequences). Use 'blastp' for protein-to-protein comparisons (amino acid sequences). The program you select should match the type of sequence you're inputting and the database you want to search against.
The E-value (Expect value) represents the number of matches you would expect to see by chance when searching a database of a particular size. A lower E-value indicates a more significant match. Generally, E-values less than 1e-5 (0.00001) suggest a very significant match, while values closer to 1 may represent random similarity.
Word size refers to the length of the initial exact matches that BLAST uses to begin its search. A larger word size makes the search faster but potentially less sensitive for finding distant relationships. For nucleotide searches, the default is usually 11, while for protein searches it's typically 3. Decreasing the word size may help find more distant matches but will increase processing time.
Search times vary widely depending on query sequence length, database size, server load, and parameter settings. Short sequences against smaller databases might complete in seconds, while longer sequences or broader searches may take several minutes. The tool provides a progress indicator for monitoring your search status.