checktrans reads a protein sequence containing stop characters and writes a statistical report of any open reading frames (ORFs) that are greater than a minimum size. An open reading frame is defined as a continuous region of protein sequence with no stop characters. The default minimum ORF size is 100 residues. In addition to the report output, any ORF sequences are written to file and features of those sequences written to a separate file.
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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. 'X13776_1_7').
A reading frame is a relative position in DNA or RNA from which contiguous, non-overlapping codons are read during transcription. There are 3 possible reading frames in mRNA strand and six in a double stranded DNA where transcription is possible from either strand. An open reading frame (ORF) is a reading frame that begins with a start codon and includes the subsequent transcribed region, stopping immediately before the first stop codon.
Where you have a nucleotide sequence for analysis, it should first be translated by using transeq. The transeq output file will then serve as the input to checktrans. Note that if you have only translated a nucleic sequence in one frame, checktrans will miss possible ORFs in the other frames. You must provide checktrans with translations in all three (six?) frames in order for it to be effective at finding all possible ORFs.