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usearch_seq
Martin Asser Hansen edited this page Oct 2, 2015
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Sequences in the stream can be used to query a database in a FASTA file usearch_seq. The resulting hit records will look like this:
REC_TYPE: USEARCH
Q_ID: test
S_ID: test_rc
IDENT: 100.0
ALIGN_LEN: 59
MISMATCHES: 0
GAPS: 0
Q_BEG: 0
Q_END: 58
S_BEG: 0
S_END: 58
E_VAL: *
SCORE: *
STRAND: -
---
Global and local search programs are available. Both strands are searched.
Usearch v7.0.1001 or later must be installed in order for usearch_seq to work.
Read more here:
http://www.drive5.com/usearch/
... | usearch_seq [options]
[-? | --help] # Print full usage description.
[-p <string> | --program=<string>] # Usearch program <global|local> - Default=global
[-d <file!> | --database=<file!>] # Database to search (FASTA file).
[-i <float> | --identity=<float>] # Minimum identity between 0 and 1.
[-e <float> | --e_val=<float>] # Maximum E-value.
[-m <uint> | --maxaccepts=<uint>] # Maximum hits to report - Default=0 (all)
[-c <uint> | --cpus=<uint>] # Number of CPUs to use - Default=1
[-I <file!> | --stream_in=<file!>] # Read input from stream file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output to stream file - Default=STDOUT
[-v | --verbose] # Verbose output.
Conducting a global search:
read_fasta -i query.fna | usearch_seq -d database.fna -i 0.97
and a local search:
read_fasta -i query.fna | usearch_seq -p local -d database.fna -i 0.9
Martin Asser Hansen - Copyright (C) - All rights reserved.
September 2013
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
usearch_seq is part of the Biopieces framework.