This program finds and outputs the sequences of open reading frames (ORFs) in one or more nucleotide sequences. An ORF may be defined as a region of a specified minimum size between two STOP codons, or between a START and a STOP codon. The ORFs can be output as the nucleotide sequence or as the protein translation. Optionally, the program will output the region around the START codon, the first STOP codon, or the final STOP codon of an ORF. The START and STOP codons are defined in a Genetic Code table; a suitable table can be selected for the organism you are investigating. The output is a sequence file containing predicted open reading frames longer than the minimum size, which defaults to 30 bases (i.e. 10 amino acids).
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The name of the ORF sequences is constructed from the name of the input sequence with an underscore character ('_') and a unique ordinal number of the ORF found appended. The description of the output ORF sequence is constructed from the description of the input sequence with the start and end positions of the ORF prepended.
The unique number appended to the name is simply used to create new unique sequence names, it does not imply any further information indicating any order, positioning or sense-strand of the ORFs.
If the ORF has been found in the reverse sense, then the start position will be smaller than the end position. The numbering uses the forward-sense positions, but read in the reverse sense. For example, >V00294_3 [465 - 49] in the output above is a reverse-sense ORF running from position 465 to 49. The description will also contain '(REVERSE SENSE)'.
If the sequence has been specified as a circular genome (using the command-line switch '-circular'), then ORFs can potentially continue past the 'end' of the input sequence (the breakpoint of the circular genome) and into the 'start' of the sequence again. This is dealt with by appending the sequence to itself three times and reporting long ORFs that are found in this extended sequence. Any ORF that is longer that three times the sequence length (i.e one that continues without hitting a STOP at any point in the genome) will be reported as being a maximum of three times the length of the input sequence. Note that the end position of an ORF in circular genomes can be apparently longer than the input sequence if the ORF crosses the breakpoint. If the ORF crosses the breakpoint, then the text '(ORF crosses the breakpoint)' will be added to the description of the output sequence.
The default file EGC.0 is the 'Standard Code' with the rarely used alternate START codons omitted, it only has the normal 'AUG' START codon. The 'Standard Code' with the rarely used alternate START codons included is Genetic Code file EGC.1.
It is expected that user will sometimes wish to customise a Genetic Code file. To do this, use the program embossdata.
There are two common definitions of an open reading frame: it can either be a region that is free of STOP codons or a region that begins with a START codon and ends with a STOP codon.