If a nucleotide query is used with a protein database, a translated
search is performed. Each ORF in the
nucleotide sequence is translated, and the resulting amino acid
sequences are used to search the database. Translated searches are
supported by most search commands. Metagenomic gene search with
ublast is the most common use
Each ORF is an independent search, so
termination conditions are
applied separately. (Note that termination conditions
are disabled by default in ublast). This is because a single
nucleotide sequence may span more than one gene. The ‑orfstyle and
‑mincodons options control ORF identification.
Currently, USEARCH does not extend
alignments through frame-shifts, though
two adjacent hits in different frames may be found, allowing
frame-shifts to be inferred. Please let me know if you need better
support for frame-shifts.
Translated searches with a nucleotide
query and nucleotide database (like TBLASTX), or with a protein
query and nucleotide database (like TBLASTN) are not supported
directly. See quick start for BLAST
users. These cases can be handled by using findorfs with ‑xlat
and using protein search on the amino acid sequences.