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. |
|