ORF Finder

What is ORF Finder?

An open reading frame (ORF) is a DNA region that can be translated without encountering an in-frame termination signal. ProteinIQ runs the native NCBI ORFfinder 0.4.3 executable, the same scientific engine distributed by NCBI, rather than reproducing its search algorithm.

The search can inspect three reading frames on the forward strand, three on the reverse strand, or a selected strand only. The selected NCBI genetic code controls translation, alternative initiation codons, and termination behavior.

An ORF is a candidate coding region, not proof of a functional gene. Expression, conservation, gene context, and splice-aware evidence are usually needed for annotation.

Input

Submit raw DNA or one or more FASTA records. IUPAC ambiguity symbols are preserved, so their coordinates remain stable and ambiguous translated codons can appear as X. Gaps, punctuation, amino-acid characters, and other invalid symbols are rejected instead of silently removed.

Input	Limit
DNA sequence	Up to 10 MB and 10,000,000 nucleotides per job
FASTA records	Up to 500 records with unique identifiers

For sequences longer than 20,000 nt, the interactive result still shows complete ORF tracks but omits nucleotide-by-nucleotide rendering. All native output files remain complete.

To keep result transfer and browser rendering reliable, one job can return at most 10,000 ORFs and 50 MB of combined native output. If a search exceeds either bound, increase the minimum ORF length or narrow the search region. Interactive tracks show the first 1,000 ORFs per sequence; the table and native files remain complete for successful jobs.

Settings

Setting	Native behavior
Minimum ORF length	Maps to -ml. Presets are 30, 75, 150, 300, and 600 nt; 75 nt is the default. A terminating stop triplet does not count toward the coding-length threshold.
Genetic code	Maps to -g. The 26 choices match the current NCBI ORFfinder web application.
Start codon mode	Maps to -s: ATG only, ATG plus alternatives defined by the selected genetic code, or any sense codon.
Strand	Maps to -strand: both, plus, or minus.
Ignore nested ORFs	Maps to native -n containment filtering.
Start position	Maps to -b; inclusive and 1-based.
End position	Maps to -e; inclusive, with 0 meaning the end of each sequence.

The source also has an experimental circular-sequence flag. NCBI marks it as under development, so it is not offered here.

Results

The ORF explorer opens with a full-sequence map. Select an ORF to zoom into its region and see its coordinates, protein sequence, and oriented DNA sequence. Use the zoom controls to inspect individual bases, or select Full sequence to return to the overview. Hover over the map to mark a base position across all six reading frames. The ORF table provides search, strand and source-status filters, sorting, and CSV export. Summary shows totals across all input sequences and links the longest ORF back to the explorer.

These views are derived from the native protein and CDS FASTA records. They preserve native ORF order and biological direction:

• forward-strand coordinates ascend from start to end;
• reverse-strand coordinates descend from start to end;
• Not marked partial means NCBI ORFfinder did not mark the protein record as partial;
• Marked partial is the source annotation, not an inference based only on the last codon;
• first and last codons are shown exactly as they occur in the oriented native CDS.

Filters and CSV/JSON exports are convenience views over those native values.

Native files

Every run includes all output formats produced by the NCBI executable:

File	ORFfinder format	Contents
Protein FASTA	-outfmt 0	Native protein translations, headers, order, and partial labels
CDS FASTA	-outfmt 1	Native oriented coding DNA sequences and source coordinates
Text ASN.1	-outfmt 2	Native sequence annotations and partial-location semantics
Feature table	-outfmt 3	Native five-column feature table
Run log	Additive	Pinned version, effective flags, and native diagnostics

ORF Finder examples

Human HBB transcript: a single standard-code ORF

This example searches the curated human beta-globin transcript for its main protein-coding region while retaining the transcript's untranslated sequence context.

• Input: Human HBB transcript, NCBI NM_000518.5 (628 nt)
• Non-default settings: Minimum ORF length = 300 nt and Strand = Forward only (+) to focus the result on the annotated coding orientation

ORF Finder returns one frame +3 ORF from positions 51–494. The native coding sequence is 444 nt and its protein translation is 147 aa. The visual map keeps the 5′ and 3′ untranslated sequence visible around the ORF, which makes the transcript context clear. This result identifies a translatable region in the submitted sequence; it does not by itself demonstrate expression or confirm transcript abundance in a biological sample.

Human ATP8/ATP6: overlapping mitochondrial reading frames

The human mitochondrial ATP8 and ATP6 genes overlap but use different reading frames. This example shows why the biological source and genetic code matter when interpreting ORF boundaries and translations.

• Input: Human mitochondrial reference NC_012920.1, positions 8366–9207 (842 nt)
• Non-default settings: Minimum ORF length = 150 nt, Genetic code = 2. Vertebrate Mitochondrial, and Start codon mode = ATG + code-specific alternative starts

The frame +1 ORF spans positions 1–207 and returns 207 nt / 68 aa. The frame +3 ORF spans positions 162–842 and returns 681 nt / 226 aa. Their 46 nt overlap is visible directly in the track view. These translations use the vertebrate mitochondrial code; applying the standard nuclear code can change termination and amino-acid assignments.

E. coli lacI: reverse-strand detection with an alternative start

This genomic-region example demonstrates reverse-strand coordinates and a code-specific alternative initiation codon around the E. coli K-12 lacI locus.

• Input: E. coli K-12 reference NC_000913.3, positions 366301–367650 (1,350 nt)
• Non-default settings: Minimum ORF length = 300 nt, Genetic code = 11. Bacterial, Archaeal and Plant Plastid, Start codon mode = ATG + code-specific alternative starts, Strand = Reverse only (-), and Ignore nested ORFs = enabled

Both returned ORFs lie on the reverse strand. The longer frame -3 ORF covers most of the submitted region, while the shorter frame -2 ORF occupies a separate interval near the high-coordinate end.

The table makes the strand direction explicit: the 1,092 nt / 363 aa ORF runs from position 1,219 down to 128 and begins with GTG, an accepted alternative start under genetic code 11. The second ORF runs from 1,277 down to 960 and returns 318 nt / 105 aa with an ATG start. Descending coordinates are expected for reverse-strand features; ORF detection alone does not establish promoter activity, expression, or regulatory function.

Genetic codes

Choose the table that matches the biological source. Examples include:

Code	Name	Notable behavior
1	Standard	TAA, TAG, and TGA terminate translation
2	Vertebrate Mitochondrial	TGA encodes Trp; AGA and AGG terminate
3	Yeast Mitochondrial	ATA and GTG can initiate; TGA encodes Trp
6	Ciliate Nuclear	TAA and TAG encode Gln
11	Bacterial, Archaeal and Plant Plastid	Includes several code-specific alternative starts
26	Pachysolen Nuclear	CTG can initiate and encodes Ala internally

Using the wrong genetic code can change ORF boundaries, translations, and reported start sites.

Interpreting ORFs

• Longer ORFs are less likely to occur by chance, but length alone is not evidence of function.
• Prokaryotic ORFs often correspond closely to coding sequences.
• Eukaryotic genes with introns require splice-aware gene prediction; ORFfinder searches continuous submitted DNA.
• Compare candidates with conserved proteins, transcript evidence, codon usage, and genomic context before assigning function.