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.\"
.\" $Id: 6ft.1,v 1.2 2003/08/11 12:09:14 vflegel Exp $
.\" Copyright (c) 2003 SIB Swiss Institute of Bioinformatics <pftools@sib.swiss>
.\" Process this file with
.\" groff -man -Tascii <name>
.\" for ascii output or
.\" groff -man -Tps <name>
.\" for postscript output
.\"
.TH 6FT 1 "May 2003" "pftools 2.3" "pftools"
.\" ------------------------------------------------
.\" Name section
.\" ------------------------------------------------
.SH NAME
6ft \- 6-frame translation of a DNA sequence into protein
.\" ------------------------------------------------
.\" Synopsis section
.\" ------------------------------------------------
.SH SYNOPSIS
.TP 10
.B 6ft
[
.B \-h
] [
.B \-r
|
.B \-s
] [
.B \-W
.I width
]
.B <
.I sequence_library
.\" ------------------------------------------------
.\" Description section
.\" ------------------------------------------------
.SH DESCRIPTION
.B 6ft
translates all six reading frames of a double-stranded DNA sequence into
individual protein sequences.
Stop codons are represented by character
.RB \(dq O \(dq.
The program
.B 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
.RB ' < '
as shown in the
.I synopsis
section.
The
.I sequence_library
contains one or several sequences in Pearson/Fasta format.
.LP
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
.BR 2ft (1),
.I see
manual pages of pftools programs
.BR ptof (1)
and
.BR 2ft (1).
.\" ------------------------------------------------
.\" Options section
.\" ------------------------------------------------
.SH OPTIONS
.\" --- h ---
.TP
.B \-h
Display usage help text.
.\" --- r ---
.TP
.B \-r
Translate only reverse (antisense) strand.
.br
This option is mutualy exclusive with option
.BR \-s .
.br
Default: translate both strands
.\" --- s ---
.TP
.B \-s
Translate only sense strand.
.br
This option is mutualy exclusive with option
.BR \-r .
.br
Default: translate both strands
.\" --- W ---
.TP
.BI \-W\ width
Set sequence output width.
.br
The value of
.RI ' width '
specifies how many residues will be output on one line.
.br
Type: integer
.br
Default: 60
.\" ------------------------------------------------
.\" Examples section
.\" ------------------------------------------------
.SH EXAMPLES
.I See
manual pages of pftools program
.BR ptof (1).
.\" ------------------------------------------------
.\" See also section
.\" ------------------------------------------------
.SH "SEE ALSO"
.BR ptof (1),
.BR pfsearch (1),
.BR pfscan (1)
.\" ------------------------------------------------
.\" Author section
.\" ------------------------------------------------
.SH AUTHOR
The
.B pftools
package was developed by Philipp Bucher.
.br
Any comments or suggestions should be addressed to <pftools@sib.swiss>.
|
