checktrans
Function
Description
Reads in a protein sequence containing stops, and writes a report of any
open reading frames (continuous protein sequence with no stops) that are
greater than a minimum size. The default minimum ORF size is 100
residues. It writes out any ORF sequences.
The input sequence might typically have been produced by transeq.
Note that if you have only translated a nucleic sequence in one frame,
checktrans will miss possible ORFs in other frames. You have to
give checktrans translations in all three (six?) frames in order
for it to be effective at finding all possible ORFs.
Usage
Command line arguments
Input file format
This program reads the USA of a protein sequence with STOP codons in it.
Output file format
This program writes three files: the ORF report file
(paamir_1.checktrans), the output sequence file (paamir_1.fasta) and the
feature file (paamir_1.out3) which is in GFF format by default.
The ORF report file gives the numeric count of the ORF, the position of
the terminating STOP codon, the length of the ORF, its start and end
positions and the name of the sequence it has been written out as.
The name of the output sequences is constructed from the name of the
input sequence followed by an underscore and then the numeric count of
the ORF (e.g. 'PAAMIR_1_7').
Data files
None.
Notes
None.
References
None.
Warnings
None.
Diagnostic Error Messages
None.
Exit status
This program always exits with a status of 0.
Known bugs
None.
Author(s)
and modified by
to output the sequence data to a single file in the conventional
EMBOSS style.
History
Target users
Comments