2ft - 2-frame translation of a DNA sequence into protein
- 2ft
- [ -h ] [ -r | -s ] [ -W
width ] < sequence_library
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).
- -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)
The
pftools package was developed by Philipp Bucher.
Any comments or suggestions should be addressed to
<
[email protected]>.