DNA Protein Translator and ORF Finder

The input is uppercased, FASTA header lines and whitespace are removed, and RNA U bases are converted to DNA T bases. Auto mode rejects a mixed T and U alphabet because the sequence cannot be classified cleanly.

Translate mode uses the NCBI Standard Code, transl_table 1. Each full codon is translated in the three forward frames and the three reverse-complement frames. Ambiguous codons are translated as X, trailing incomplete codons are omitted and reported, and stop codons remain visible as asterisks.

The ORF finder scans all six frames, opening at a start codon (ATG by default, optionally GTG or TTG) and closing at the first in-frame stop, reporting the longest open reading frame per stop. Length includes the stop codon; coordinates are 1-based on the plus strand, and a reverse-strand ORF reads start greater than end. The minimum length defaults to 75 nt and is adjustable.

Melting temperature uses the Wallace 2 plus 4 rule below 14 nt and the SantaLucia 1998 nearest-neighbor model at 14 nt and up, with adjustable sodium and oligo concentration and a stated salt correction. The active model and its valid length range are shown. Tm mode takes an unambiguous DNA A, C, G, and T oligo; RNA duplex melting uses different nearest-neighbor parameters, so RNA is rejected. GC content is reported as G plus C over the unambiguous bases, available on its own as GC content mode.

Formula: six-frame translation, ORF scan, Wallace and nearest-neighbor Tm, GC content

See Sources below