Characterize Unknown Sequence
Paste any unknown sequence and get a full identity report, then send it to BLAST.
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.
Design, edit, and verify complete constructsSeqStudio combines sequence editing and annotation, plasmid maps, primer/cloning/CRISPR design, Sanger verification, and GenBank/SnapGene files in one workspace.
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.
Can I run this from code?
Yes — the same report is available via the REST API and the MCP server.
More
Guides
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