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fastacmd - Online in the Cloud

Run fastacmd in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command fastacmd that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


fastacmd - retrieve FASTA sequences from a BLAST database

SYNOPSIS


fastacmd [-] [-D N] [-I] [-L start,stop] [-P N] [-S N] [-T] [-a] [-c] [-d str] [-i str]
[-l N] [-o filename] [-p type] [-s str] [-t]

DESCRIPTION


fastacmd retrieves FASTA formatted sequences from a blast(1) database formatted using the
`-o' option. An example fastacmd call would be

fastacmd -d nr -s p38398

OPTIONS


A summary of options is included below.

- Print usage message

-D N Dump the entire database in some format:
1 fasta
2 GI list
3 Accession.version list

-I Print database information only (overrides all other options)

-L start,stop
Range of sequence to extract (0 in start is beginning of sequence, 0 in stop is end
of sequence, default is whole sequence)

-P N Retrieve sequences with Protein Identification Group (PIG) N.

-S N Strand on subsequence (nucleotide only):
1 top (default)
2 bottom

-T Print taxonomic information for requested sequence(s)

-a Retrieve duplicate accessions

-c Use ^A (\001) as non-redundant defline separator

-d str Database (default is nr)

-i str Input file with GIs/accessions/loci for batch retrieval

-l N Line length for sequence (default = 80)

-o filename
Output file (default = stdout)

-p type
Type of file:
G guess (default): look for protein, then nucleotide
T protein
F nucleotide

-s str Comma-delimited search string(s). GIs, accessions, loci, or fullSeq-id strings may
be used, e.g., 555, AC147927, 'gnl|dbname|tag'

-t Definition line should contain target GI only

EXIT STATUS


0 Completed successfully.
1 An error (other than those below) occurred.
2 The BLAST database was not found.
3 A search (accession, GI, or taxonomy info) failed.
4 No taxonomy database was found.

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