-orfstyle
The orfstyle and mincodons options control how ORFs are identified by USEARCH. These options are used by the findorfs command and by translated searches .
The value of orfstyle is an integer obtained by adding the numbers from the table below. The default value of orfstyle is 5.
| Value | Description | |
| 1 | Allow an ORF to start at the beginning of the nucleotide sequence (otherwise, must begin with a START codon). | |
| 2 | Allow an ORF to start immediately following a STOP codon (otherwise, must begin with a START codon). This compensates for read errors that might corrupt a START codon sequence, and allows non-standard START codons. | |
| 4 | Allow an ORF to end at the end of the nucleotide sequence (otherwise, must be terminated by a STOP codon). | |
| 8 | Include the STOP codon, if any, in the translated sequence. This is useful in the findorfs command to distinguish ORFs that contain a STOP from those that are terminated by the end of the nucleotide sequence. The STOP codon is represented by an asterisk (*). Do not use for translated searches. |
