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Codon Alignment Explanation

What is Codon Alignment?

When aligning DNA sequences, most algorithms only consider the best alignment for the nucleotide residues. The process of codon alignment considers the reading frame of the translated protein and adjusts the nucleotide alignment so that the protein alignment stays in frame.

Specifically, this tool may make the following adjustments to your input alignment:

Example

All 3 of these adjustments are illustrated in the example below. This input alignment has an open reading frame that begins in Frame 1, but is not codon-aligned:

Reference   ATG-AGAGTGAAGGAG--CAGGAAGAATTATCAGCACTTGTGGAGATGGT-GGTG
Sequence2   ATG-AGAGTCAAGGGG--CAGGAAGAATTATCAGCACTTGTGGAGATGGT-GGTG
Sequence3   ATGAAGAGTGAAGGAGATCAGGAAGAAATATCAG------TGGAGATGGTGGGTG

This is the output from the Codon Alignment tool, produced with default parameters:

Reference  ATG---AGAGTGAAGGAGCAGGAAGAATTATCAGCACTTGTGGAGATGGTG---GTG
           _M__-__R__V__K__E__Q__E__E__L__S__A__L__V__E__M__V__-__V_
Sequence2  ATG---AGAGTCAAGGGGCAGGAAGAATTATCAGCACTTGTGGAGATGGTG---GTG
           _M__-__R__V__K__G__Q__E__E__L__S__A__L__V__E__M__V__-__V_
Sequence3  ATGAAGAGTGAAGGAGATCAGGAAGAAATATCA------GTGGAGATGGTGG--GTG
           _M__K__S__E__G__D__Q__E__E__I__S__-__-__V__E__M__V__#__V_

Input
Options
Output

The output will provide:


Related Programs
last modified: Tue Nov 20 13:31 2012


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