NAME

       6ft - 6-frame translation of a DNA sequence into protein

SYNOPSIS

       6ft       [ -h ] [ -r | -s ] [ -W width ] < sequence_library

DESCRIPTION

       6ft  translates  all  six  reading  frames  of  a  double-stranded  DNA  sequence into individual protein
       sequences.  Stop codons are represented by character "O".  The program 6ft reads  input  fasta  formatted
       DNA  sequences from standard input. If the sequences are contained in a file, the input can be redirected
       from this file  using  the  shell's  input  redirector  '<'  as  shown  in  the  synopsis  section.   The
       sequence_library contains one or several sequences in Pearson/Fasta format.

       This  program  may be used for searching genomic or EST sequence databases with a protein profile. Better
       results are usually obtained by first converting the protein profile into  a  frame-search  profile,  and
       then  searching a 2-frame translation of the DNA sequence database generated with pftools program 2ft(1),
       see manual pages of pftools programs ptof(1) and 2ft(1).

OPTIONS

       -h     Display usage help text.

       -r     Translate only reverse (antisense) strand.
              This option is mutualy exclusive with option -s.
              Default: translate both strands

       -s     Translate only sense strand.
              This option is mutualy exclusive with option -r.
              Default: translate both strands

       -W width
              Set sequence output width.
              The value of 'width' specifies how many residues will be output on one line.
              Type: integer
              Default: 60

EXAMPLES

       See manual pages of pftools program ptof(1).

SEE ALSO

       ptof(1), pfsearch(1), pfscan(1)

AUTHOR

       The pftools package was developed by Philipp Bucher.
       Any comments or suggestions should be addressed to <pftools@sib.swiss>.

pftools 2.3                                         May 2003                                              6FT(1)