Open reading frame parameters

This opens the dialog displayed in figure 16.8:

Image readingframenext
Figure 16.8: Create Reading Frame dialog.

The adjustable parameters for the search are:

Using open reading frames for gene finding is a fairly simple approach which is likely to predict genes which are not real. Setting a relatively high minimum length of the ORFs will reduce the number of false positive predictions, but at the same time short genes may be missed (see figure 16.9).

Image orf_coli
Figure 16.9: The first 12,000 positions of the E. coli sequence NC_000913 downloaded from GenBank. The blue (dark) annotations are the genes while the yellow (brighter) annotations are the ORFs with a length of at least 100 amino acids. On the positive strand around position 11,000, a gene starts before the ORF. This is due to the use of the standard genetic code rather than the bacterial code. This particular gene starts with CTG, which is a start codon in bacteria. Two short genes are entirely missing, while a handful of open reading frames do not correspond to any of the annotated genes.

Click Next if you wish to adjust how to handle the results. If not, click Finish.

Finding open reading frames is often a good first step in annotating sequences such as cloning vectors or bacterial genomes. For eukaryotic genes, ORF determination may not always be very helpful since the intron/exon structure is not part of the algorithm.