open reading frames
An open reading frame (ORF) is a segment of a nucleotide sequence that begins with a start codon, ends with a stop codon and is long enough to code for a protein. In USEARCH, the minimum number of amino acid codons in an ORF is set by the - mincodons option, default value 20.
With a nucleotide query sequence and amino acid database, USEARCH performs a translated search . ORFs are identified in the nucleotide sequence, and each ORF is treated as a separate query with its own termination conditions . This is because a single nucleotide sequence may span more than one gene.
