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From CAGT

Frame Splitter


  • Aim:
    Identify conserved codons where the amino acid permits 4-fold degeneracy on the third nucleotide

  • Method:
    Multiple alignment is partitioned into codons. The first codon starts at the first position of the multiple alignment. We report codon positions (columns) which meet the following criteria:

    1. Every codon in the column specifies the same amino acid.
    2. The amino acid has 4 or more codons.
    3. Every codon in the column is the same.
    4. The codon belongs to a group with 4-fold degeneracy:
      Thr, Pro, Gly, Ala, Val, Arg (CGx), Leu (CTx), Ser (TCx).

  • Output:

    1. The output is a histogram of the multiple alignment showing columns that meet the criteria above if window size equals 1. If window size is greater than 1, histogram shows count of successful columns within consecutive windows.
    2. Tabular output showing the position and the amino acid of each conserved codon.


Version 1.0. Last revision date March 1, 2005.
Questions or comments to Gary Benson.

Protein Engineering