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Open Reading Frame Finder

ORF finder searches for open reading frames (ORFs) in the DNA sequence you enter. The program returns the range of each ORF, along with its protein translation. Use ORF finder to search newly sequenced DNA for potential protein encoding segments, verify predicted protein using newly developed SMART BLAST or regular BLASTP.

This web version of the ORF finder is limited to the subrange of the query sequence up to 50 kb long. Stand-alone version, which doesn't have query sequence length limitation, is available for Linux x64.

Examples (click to set values, then click Submit button) :

NC_011604 Salmonella enterica plasmid pWES-1; genetic code: 11; 'ATG' and alternative initiation codons; minimal ORF length: 300 nt
NM_000059; genetic code: 1; start codon: 'ATG only'; minimal ORF length: 150 nt

Enter Query Sequence

Enter accession number, gi, or nucleotide sequence in FASTA format: [?]

Enter query sequence in the text area. No hyphens are allowed. To determine the format of the input automatically, certain conventions are required with regard to the input of identifiers. See Accepted Input Formats for more details.

[?]

Enter coordinates for a subrange of the query sequence. The ORF search will apply only to the residues in the range. Sequence coordinates are from 1 to the sequence length. The range includes the residue at the To coordinate.

From: To:

Choose Search Parameters

Minimal ORF length (nt): [?]

The search will be restricted to the ORFs with the length equal or more than the selected value

Genetic code: [?]

The Genetic Codes are described here

ORF start codon to use: [?]

Use 'ATG' only as ORF start codon, or all alternative start codons, corresponding to the selected genetic code, or any sense codon (find all stop-to-stop ORFs)

"ATG" only

"ATG" and alternative initiation codons

Any sense codon

Ignore nested ORFs: [?]

If checked - ignore the ORFs completely placed within another

Start Search / Clear