Distances writes a matrix of the pairwise evolutionary distances between aligned sequences. Gene Finding CodonPreference finds possible protein coding regions. Third position bias in the codon can also be displayed. TestCode plots a measure of the non-randomness of the composition at every third base. TestCode uses the statistical method of Fickett based on the period three compositional constraints in the entire nucleic acid database to identify and display protein coding regions.
Frames displays open reading frames for the six DNA translation frames.
Frames displays open reading frames for the six DNA translation frames. PlotFold's energy dotplot is a two-dimensional graph where both axes represent the same RNA sequence and each point on the graph indicates a base pair between the ribonucleotides whose positions in the sequence are the coordinates of that point on the graph. PlotFold's circles plot is a circular Nussinov graph of a nucleic secondary structure that shows the sequence as a segment of the circle. PlotFold's squiggles plot represents the bonds formed between bases as chords. Translation Nucleotide sequences are translated into peptides using the Translate program.