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 over-

     lapping  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  redi-

     rected from this file using the shell's input redirector '<'

     as shown in the synopsis section.  The sequence_library con-

     tains 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 developped by Philipp Bucher.

     Any  comments  or  suggestions  should   be   addressed   to

     <pftools@isb-sib.ch>.