ORF finder
Tools
- Sequence stats
- Reverse complement
- FASTA/FASTQ format validator
- FASTQ → FASTA
- FASTA ID deduplicator
- DNA ↔ RNA converter
- FASTA length filter
- FASTA splitter
- FASTA header extractor
- GC content calculator
- Nucleotide frequency
- Sequence line wrapper
- DNA → Protein translation
- ORF finder
Identify open reading frames (ORFs) in DNA or RNA across all 6 reading frames, with support for multi-sequence FASTA, alternative genetic codes, interactive visualization, and nucleotide or peptide FASTA export.
Results
About this tool
Detects open reading frames (ORFs) in DNA or RNA sequences across all 6 reading frames, reporting strand, frame, genomic coordinates, nucleotide length, amino-acid length, and translated peptide.
Supports both compact (NCBI-like) enumeration and an optional exhaustive mode that includes all valid internal start codons reaching the same downstream stop, as well as optional removal of nested ORFs.
Results are linked across an interactive ORF map, sortable table, and FASTA views, allowing rapid inspection and comparison of ORFs within and across sequences.
Accepts multi-sequence FASTA input and exports nucleotide and peptide FASTA for all detected ORFs, enabling downstream analysis without additional preprocessing.
Large result sets may be previewed only partially in the browser for responsiveness. Downloads always contain the complete ORF table and full nucleotide and peptide FASTA outputs.
For larger datasets, multi-file runs, or more involved workflows, this can be executed separately as a custom analysis.
Details
An open reading frame (ORF) is a contiguous coding interval in one reading frame. In this tool, coordinates are always reported on the original submitted sequence, including reverse-strand ORFs. For a quick refresher on accepted DNA and RNA symbols, see the sequence alphabets reference.
ATG / AUG only reports ORFs that begin at ATG (or AUG in RNA) and continue to the first in-frame stop codon.
ATG / AUG + alternative starts also allows alternative initiation codons supported by the selected NCBI genetic code.
Any sense codon reports stop-to-stop ORFs. This mode is useful for scanning uninterrupted coding intervals without requiring a canonical start codon.
Compact enumeration keeps only the earliest valid start codon before a downstream stop. This usually produces a smaller, cleaner ORF set and is closer to common ORF-finder defaults.
All valid starts to same stop also reports internal valid start codons that reach that same downstream stop. This usually produces a larger set of overlapping ORFs.
Compact: report only the longer ORF starting at the first ATG.
All valid starts to same stop: report both the longer ORF and the shorter internal ORF if both satisfy the minimum length threshold.
Nested ORF filtering removes ORFs whose coordinates are completely contained within a larger ORF on the same strand.
Nested ORF: 180 -------------- 300
With nested filtering off, both ORFs are reported. With nested filtering on, the shorter fully contained ORF is removed.
- scan assembled contigs for candidate coding regions
- inspect the longest ORF in plasmids, amplicons, or viral segments
- compare forward and reverse reading-frame content
- export putative peptide sequences for downstream similarity searches
- explore alternative initiation sites using exhaustive internal-start mode
ORF finding is a useful first-pass inspection step, but it is not gene prediction. Long ORFs can occur by chance, and start-codon presence alone does not prove a protein-coding gene.
Results depend on the selected genetic code, minimum length threshold, and enumeration mode. More permissive settings generally increase ORF counts.
Unlike many ORF finder tools, this implementation:
- accepts multi-sequence FASTA input without preprocessing
- provides explicit control over ORF enumeration strategies
- allows removal of nested ORFs as a separate filtering step
- links ORF visualization, tabular inspection, and FASTA output
For direct frame-by-frame protein translation without ORF calling, use the DNA to protein translation tool.
To inspect nucleotide composition before or after ORF analysis, see the GC content calculator, nucleotide frequency tool, or sequence stats.
