NAME

       2ft - 2-frame translation of a DNA sequence into protein

SYNOPSIS

       2ft       [ -h ] [ -r | -s ] [ -W width ] < sequence_library

DESCRIPTION

       2ft   converts   both   strands   of   one   or   several  DNA  sequences  into  so-called
       "interleaved frame-translated"  DNA  sequences.   An  "interleaved frame-translated"   DNA
       sequence is an amino acid sequence of translated overlapping codons. For instance, the DNA
       sequence "ATGGCA" consisting of four overlapping codons would be translated into the amino
       acid  sequence  "MWGA",  representing  the translation of the 1st codon of the 1st reading
       frame, the 1st codon of the 2nd reading frame, the 1st codon of the 3rd reading frame  and
       the 2nd codon of the 1st reading frame.  Stop codons are represented by the character "O".
       The program 2ft reads 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  is  used  for searching genomic or EST sequence databases with frame-search
       profiles generated by pftools program ptof(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)

AUTHOR

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