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       fastacmd - retrieve FASTA sequences from a BLAST database


       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]


       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


       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

       -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,

       -t     Definition line should contain target GI only


              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.


       The National Center for Biotechnology Information.


       blast(1), /usr/share/doc/blast2/fastacmd.html.