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For the shift-frame gap-opening events, the 'QStart' value is the value for the first codon of a predicted ORF overlapping with the gap-opening sequence. For the shift-frame events, a value of '1' indicates that the start codon overlaps the gap-opening sequence. For the ORF-frame events, a value of '0' indicates that an ORF overlaps the gap-opening sequence, and '1' indicates that the start codon does not overlap the gap-opening sequence. This analysis tool can be used to validate gene predictions by identifying errors or artifacts of gene prediction pipelines from overlapping with PRF sites. However, there are inherent biases in the codon usage of eukaryotic genomes and to identify these, input of codon usage profiles (e.g. *.gc2 files) is required. The annotated genome should be provided in a FASTA format.
NOTE: A gap of any length between two possible open reading frames will be considered a potential frameshift event. It is important to bear in mind that the codon usage bias for eukaryotic genomes will influence the "codon quality score" and affect the identification of frameshift sites. For example, the genomes of trypanosomes contain TTT, TTA, TTC, GTT, CTG, CTC, and CTT as possible triplets. This means that a site which contains any of these triplets will be assigned the same score as one containing CCC or CTT. At the same time, this is a very small set of triplets. d2c66b5586
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