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ORF finder

Purpose of this page

This web page is designed to find and annotate open reading frames in a cDNA sequence. The page will try to annotate sequences containing ambiguous bases, however the start and stop codons must not contain ambiguous residues. (To see how to invert the sequence read the instructions.)

insilicase icon A Windows program that duplicates this page can be downloaded here.

Enter the cDNA sequence below and press submit (maximum length =15000kb)

     



Press the button to remove cDNA and ORF data.  

 

Instructions and example data

The page works in three steps, first enter the sequence and press the submit button, then select the ORF you wish to use. Only ORFs greater than 30 amino acids and on the forward strand will be returned. If your sequence is in the reverse orientation press to invert it. Finally, select the output formatting.

When translating codons containing ambiguous base calls it will create two alternate codons, this means that if the ambiguous base represents more than 2 bases (i.e. it is "B", "D", "H", "V" or "N") it will not correctly translate the codon unless the base is at a 'wobble' position. Similarly, if a codon contains more then 1 ambiguous position the web page does not know the phase of the mutations. This means that they will be more than two possible codons, in these situations the amino acid in the protein sequence will be derived from one possible codon, while the alternative will be set to "X" or "Xxx".

To import a test sequence press button. This sequence contains a number of ambiguous residues at the start of the ORF (593 to 2057) (on the line starting at 601bp). The first ambiguous base is an 'R' residue which is translated to a glycine or arginine. The next is a codon with two ambiguous bases which is translated to asparagine and a X since the page can not deduce the phase of each allele. The last 2 ambiguous bases involve a 'V' residue ('a', 'c' or 'g') the first is not in the wobble position while the second is. Consequently, the first 'V' residue results in a "X" or "Xxx" residue while the second is translated as a proline.



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