ORF Finder (Open Reading Frame)

An ORF is a continuous stretch of DNA that begins with a start codon (usually ATG) and ends with a stop codon (TAA, TAG, or TGA), potentially encoding a protein. ORFs are important for identifying genes and protein-coding regions in DNA sequences.

The tool supports multiple genetic codes including the standard genetic code, vertebrate mitochondrial, yeast mitochondrial, and other specialized codes. Different genetic codes use different codon-to-amino acid mappings.

Setting a minimum length helps filter out short, potentially non-functional ORFs that occur by chance. Longer ORFs are more likely to represent real protein-coding genes. Common thresholds are 150-300 nucleotides.

Nested ORFs are smaller ORFs contained within larger ones in the same reading frame. Ignoring them helps focus on the most likely protein-coding sequences and reduces redundant results.

Yes, the tool analyzes all six reading frames - three forward frames and three reverse complement frames. This ensures you don't miss ORFs encoded on either strand of the DNA.

You can input raw DNA sequences or FASTA format. The tool accepts standard nucleotide characters (A, T, G, C) and supports the complete IUPAC alphabet for ambiguous nucleotides.

ORF prediction identifies potential protein-coding regions but doesn't guarantee they are actual genes. Further analysis with tools like BLAST can help verify if predicted proteins match known sequences.

The tool can analyze sequences up to 50,000 nucleotides long. For longer sequences, consider using standalone bioinformatics software or splitting your sequence into smaller segments.