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usearch_global command
 
Search for one (default) or a few high-identity hits to a database using the USEARCH algorithm. Alignments are global. To get more than one hit, increase -maxaccepts.

An identity threshold must be specified using the ‑id option.

A database file must be specified using the ‑db option. FASTA and .udb formats are supported. For large databases, .udb format is recommended (see makeudb_usearch command).

The ‑strand option is required for nucleotide databases.

Nucleotide, protein and translated searches are supported.

See also:
  Standard output file options
 
Accept options
  Weak hits
  Termination options
  Indexing options
  Multithreading
  Masking options
  Alignment parameters
  Alignment heuristics

Examples

usearch -usearch_global query.fasta -db proteins.udb -id 0.8 -alnout results.aln
 
usearch -usearch_global query.fasta -db ESTs.fasta -id 0.9 -blast6out results.m8 \
  -strand plus -maxaccepts 8 -maxrejects 256