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fastacmd.1.gz

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  fas‐
       tacmd 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 nucleo‐
                     tide
              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.

AUTHOR
       The National Center for Biotechnology Information.

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



NCBI                         2005-11-04                  FASTACMD(1)
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