6ft - 6-frame translation of a DNA sequence into protein
- 6ft
- [ -h ] [ -r | -s ] [ -W
width ] < sequence_library
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).
- -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
See manual pages of pftools program
ptof(1).
ptof(1),
pfsearch(1),
pfscan(1)
The
pftools package was developed by Philipp Bucher.
Any comments or suggestions should be addressed to
<
[email protected]>.