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FASTACMD(1)		   NCBI	Tools User's Manual		   FASTACMD(1)

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 se-
	      quence, 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|db-
	      name|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.

AUTHOR
       The National Center for Biotechnology Information.

SEE ALSO
       blast(1), fastacmd.html.

NCBI				  2005-11-04			   FASTACMD(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | EXIT STATUS | AUTHOR | SEE ALSO

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