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CodonChanges

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CodonChanges is the algorithm for the estimation of the direction of codon changes between two previously aligned nucleotide sequences.

 

Instructions

Copy your nucleotide sequences in white cells on lists entitled "sequence1" and "sequence2".

Algorithm recognizes the following symbols: "A", "T", "G", "C" [for nucleotides] and "N" [for gaps]. No other symbols including "space", "the end of the line", "tabulation" and "the end of the paragraph" are needed. (You can easily copy aligned sequences straight from MEGA Alignment Explorer and replace symbols "-" to symbols "N")

Go to the list entitled "gene1", scroll right way and see the table with nucleotide substitutions rates from gene1 to gene2.

Type a codon in special cell in "Codon" list and see the directions of its changes in "Changes" list.

 

Please, cite

Khrustalev V.V., Barkovsky E.V. Main Pathways of Proteome Simplification in Alphaherpesviruses Under the Influence of the Strong Mutational GC-pressure // Journal of Proteomics and Bioinformatics 2009. Vol. 2. Issue 2. P.88-96.

 

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