freqAnalysis: program for the statistical analysis of nucleotide motifs

> Nucleotides
> Codons
> Amino acids
> Amino acid dimers
> Phase I heptamers
> Phase III heptamers

Analysis of S. cerevisiae

The program was applied to protein-encoding nucleotide sequences from S. cerevisiae, downloaded as the file orf_coding.fasta from the Saccharomyces Genome Database ( .) To restrict the analysis to sequences likely to express native chromosomal yeast proteins, we removed from the dataset all mitochondrial sequences, insertion sequences, and ORFs containing internal in-frame stop signals, a total of 146 sequences. The algorithm was applied to the remaining 6161 sequences (8,553,465 nucleotides), consisting of both putative and experimentally identified orfs, with input values of j (codon length) = 3, k (oligo length) = 7, and p (phase) = 1 and 3 corresponding respectively to motifs known to induce programmed +1 and -1 frameshifts.

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