freqAnalysis was designed to identify statistically aberrant k-length nucleotide motifs in coding DNA sequences, specifically to identify putative programmed translational frameshift sites. These are short sequences capable of inducing highly efficient ribosomal frameshifting by destabilizing normal ribosome-mRNA interaction. Because of the potentially catastrophic effect of frameshifting on normal protein production, we reasoned, such sites would be selected against by evolution and hence statistically underrepresented in protein-encoding sequences.
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Bioinformatics. 2002 Aug;18(8):1046-53.
Computational identification of putative programmed translational frameshift sites.
Shah AA, Giddings MC, Parvaz JB, Gesteland RF, Atkins JF, Ivanov IP.