BLAST Search — Identify a Sequence Against GenBank
Paste a sequence and find out what it is, against the whole of GenBank, with the program chosen for you.
🔒 Nothing you paste is logged or stored on our servers — Runs at NCBI: the sequence you paste is sent to NCBI's BLAST service, which performs the search.
Every other tool here compares your sequence to one you already have. This one asks the open question — what IS this? — by searching it against the whole of GenBank through NCBI's own BLAST service. Paste a colony-PCR read, an insert of unknown provenance or a protein, and the program is chosen from the sequence itself: nucleotide goes to megablast against the nucleotide collection, protein to blastp against the non-redundant protein database. Results come back as a ranked table with each hit's accession, description, organism, percent identity, expect value and how much of YOUR query it covers — with overlapping alignments merged, so coverage cannot read above 100%. A search usually takes twenty to sixty seconds; NCBI asks that a single search is checked no more than once a minute, so the page waits between checks and shows you the request id, which stays valid on their side for about a day.
0 residues. The program is chosen from the sequence: nucleotide searches GenBank with megablast, protein searches the non-redundant protein database.
Paste a sequence to search it against GenBank.
How to use the BLAST Search tool
- 1Paste a DNA or protein sequence, raw or as FASTA.
- 2Press Search — the program and database are chosen from the sequence.
- 3Read the ranked hits: identity and query coverage together tell you whether a hit explains your whole sequence or only part of it.
Frequently asked questions
What is the difference between percent identity and query coverage?
Identity is how well the matched region matches; coverage is how much of your sequence was matched at all. They answer different questions and a hit can be high in one and low in the other — a 100% identity hit covering 12% of your query means a short stretch matched perfectly and the rest of your sequence is unaccounted for. That combination is the usual signature of a shared promoter or tag rather than the gene you were looking for, which is why both are shown side by side.
Why does a search take so long?
The search runs on NCBI's machines against a database of well over a hundred million sequences, and it is queued alongside everyone else's. Twenty to sixty seconds is normal for a nucleotide search; a protein search can take several minutes. NCBI also asks that any one search is polled no more than once a minute, so this page waits between checks rather than hammering it. The request id shown while it runs stays valid on their side for about twenty-four hours.
Why does one hit say a number of identical entries?
BLAST collapses database records with the same sequence into a single hit. If your insert matches a sequence that has been deposited a dozen times under different accessions, you get one row and a count of the others, rather than twelve rows saying the same thing. The accession shown is the representative one.
Can I choose the program or database myself?
Through the API, yes — blast_submit takes a program and database. On this page the program is inferred from the sequence, because it is not really a choice: a protein query cannot be run through blastn, and passing a mismatched pair is refused with an explanation rather than quietly returning nothing.
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