freqAnalysis: program for the statistical analysis of nucleotide motifs

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> Analysis of S. cerevisiae


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.

The input to the algorithm is the set of sequence data from all putative coding sequences of a single organism. The relative codon frequencies and the relative intra-codon frequencies of the 4 nucleotides {A,C,G,T} are used to calculate a probability, or expected relative frequency, for each of the 16,384 possible combinations of two codons and a single nucleotide. The program ranks the heptamers by comparing this probability to the actual relative frequency of each heptamer as counted in the same coding sequences, in order to identify those that occur far more or less often than expected from the independent distribution of codons. Expected relative frequencies of all amino acid dimers in the translated sequences are similarly calculated from the observed amino acid bias and compared to their actual relative frequencies in order to determine the extent to which the over- or underrepresentation of nucleotide heptamers is related to their amino acid-encoding function.

The program was written in Java 2, using the Swing package for the graphical user interface. It can be run on Unix or Windows systems.

After downloading, add the name of the directory to which the jar file has been downloaded to the classpath. The program is started by typing java -jar FreqAnalysis.jar at the command prompt, or by adding the path to the jar file to the CLASSPATH and typing java FreqAnalysis .

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