Characterize Unknown Sequence
Paste any unknown sequence and get a full identity report, then send it to BLAST.
🌐 Nothing you paste is logged or stored — every tool is also callable via REST & MCP, and in bulk from the batch tools
Not sure what you are looking at? Paste any DNA, RNA or protein sequence and the Characterize Unknown Sequence tool tells you everything in one pass. It auto-detects the molecule type from the residues, then adapts the report: for nucleotides it gives length and GC content, the best (longest) open reading frame with its translated protein, restriction enzymes that cut exactly once for cloning, and suggested end primers with melting temperatures; for proteins it gives molecular weight, isoelectric point, net charge and hydropathy. A one-click "Identify with BLAST" button opens the matching NCBI blastn or blastp search with your sequence pre-filled.
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Paste a sequence above to characterize it, or load the example.
Working on a whole construct rather than one sequence? Open SeqStudio — the full editor, with live feature annotation, plasmid maps, restriction and primer panels, undo/redo, multi-document tabs and GenBank / SnapGene import and export.
How to use the Characterize Sequence tool
- 1Paste an unknown DNA, RNA or protein sequence, or a FASTA record — or click Load example.
- 2Read the auto-detected type banner and the tailored report: composition, best ORF, cloning sites and primers for nucleotides, or MW/pI/charge for proteins.
- 3Copy or download the full report, then click Identify with BLAST to search NCBI for matches.
Frequently asked questions
How does it know if my sequence is DNA, RNA or protein?
It applies a mostly-ACGT heuristic: if over 90% of the letters are canonical bases (A/C/G/T/U/N) it is called a nucleotide, and the presence of U without T marks it as RNA. Anything else is treated as a protein sequence. The detection reason is shown so you can override by editing the input.
What does the report include for a DNA or RNA sequence?
Length and GC content, the best (longest) open reading frame with its protein translation and a table of other ORFs, restriction enzymes that cut exactly once for cloning, and suggested forward/reverse end primers with melting temperatures and a Tm match check.
How do I identify what the sequence actually is?
Click Identify with BLAST. It opens NCBI BLAST in a new tab with the correct program (blastn for DNA/RNA, blastp for protein) and your sequence already filled into the query box, so you can run a homology search against the databases immediately.
Is my data stored?
No. Your sequence is used only to compute the characterization report and is never logged or stored. The same report is available via the REST API and the MCP server. Separately, only if you click Identify with BLAST is the sequence sent to NCBI's servers to run the search there.
More
Related tools
Generate composition, ORF, restriction-site and primer summaries from one sequence.
Assemble fragments and design junction primers for Gibson, Golden Gate or restriction cloning.
Apply one operation to every record in a multi-FASTA and export a single CSV/TSV table.